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pmid:27508061

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline

Yunshun Chen · Aaron T. L. Lun · Gordon K. Smyth

F1000Research · 2016 doi:10.12688/f1000research.8987.2

Abstract

In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most common aims of RNA-seq profiling is to identify genes or molecular pathways that are differentially expressed (DE) between two or more biological conditions. This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq data by providing a complete analysis of an RNA-seq experiment profiling epithelial cell subsets in the mouse mammary gland. The workflow uses R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, including alignment of read sequences, data exploration, differential expression analysis, visualization and pathway analysis. Read alignment and count quantification is conducted using the Rsubread package and the statistical analyses are performed using the edgeR package. The differential expression analysis uses the quasi-likelihood functionality of edgeR.

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Handoff: revision 4 · sha256:55ea50e300bb431a86d436951ca0ffa6f4e183dc3cde24b554526da6a21d4402

Five-stage experiment

  1. 1 Align the RNA-seq reads to the mouse mm10 genome Definition rna-seq-read-alignment · unsupported
  2. 2 Quantify the reads assigned to each gene Definition rna-seq-gene-quantification · unsupported
  3. 3 Filter low counts and normalise the libraries with TMM Definition rna-seq-count-filtering-and-normalisation · partial
  4. 4 Fit the edgeR quasi-likelihood model and control the false discovery rate Definition rna-seq-differential-expression · partial
  5. 5 Analyse the enriched GO and KEGG pathways Definition rna-seq-pathway-enrichment · supported

The order is the order the experiment runs them in. The full definitions, contracts and evidence are in the file below.

Paper

complete

Experiment

partial

Data

partial

Analysis

partial

Execution

absent

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paper object · 10 fields
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title
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
doi
10.12688/f1000research.8987.2
pmid
27508061
authors array · 3 items
[0]
Yunshun Chen
[1]
Aaron T. L. Lun
[2]
Gordon K. Smyth
journal
F1000Research
year
2016
abstract
In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most common aims of RNA-seq profiling is to identify genes or molecular pathways that are differentially expressed (DE) between two or more biological conditions. This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq data by providing a complete analysis of an RNA-seq experiment profiling epithelial cell subsets in the mouse mammary gland. The workflow uses R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, including alignment of read sequences, data exploration, differential expression analysis, visualization and pathway analysis. Read alignment and count quantification is conducted using the Rsubread package and the statistical analyses are performed using the edgeR package. The differential expression analysis uses the quasi-likelihood functionality of edgeR.
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Between basal lactating and basal pregnant mice, the edgeR quasi-likelihood F-test calls 5245 differentially expressed genes at a false discovery rate of 5%, and the top gene is Csn1s2b with a log2 fold change of 6.08.
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In order to control the false discovery rate (FDR), multiple testing correction is performed using the Benjamini-Hochberg method. The top DE gene Csn1s2b has a large positive logFC, showing that it is far more highly expressed in the basal cells of lactating than pregnant mice. This gene is indeed known to be a major source of protein in milk.
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sections[12] "Testing for differential expression" paragraph 8
quote
In order to control the false discovery rate (FDR), multiple testing correction is performed using the Benjamini-Hochberg method. The top DE gene Csn1s2b has a large positive logFC, showing that it is far more highly expressed in the basal cells of lactating than pregnant mice. This gene is indeed known to be a major source of protein in milk.
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Testing the same contrast against a fold-change threshold of 1.5 with glmTreat calls 1123 genes at a false discovery rate of 5%, and the paper states that about 1100 genes are detected.
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Note that the argument lfc is an abbreviation for “log-fold-change”. About 1100 genes are detected as DE with a FC significantly above 1.5 at an FDR cut-off of 5%.
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sections[13] "Differential expression relative to a fold-change threshold" paragraph 5
quote
Note that the argument lfc is an abbreviation for “log-fold-change”. About 1100 genes are detected as DE with a FC significantly above 1.5 at an FDR cut-off of 5%.
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The interaction between mouse status and cell type — the change from pregnant to lactating in luminal cells less the same change in basal cells — is tested with the same quasi-likelihood F-test, and the top gene is Ppl with a log2 fold change of -4.62.
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Suppose we are interested in testing whether the change in expression between lactating and pregnant mice is the same for basal cells as it is for luminal cells. In statistical terminology, this is the interaction effect between mouse status and cell type.
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sections[16] "Complicated contrasts" paragraph 2
quote
Suppose we are interested in testing whether the change in expression between lactating and pregnant mice is the same for basal cells as it is for luminal cells. In statistical terminology, this is the interaction effect between mouse status and cell type.
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The genewise count matrix the analysis starts from holds 27179 genes over twelve libraries, and the filter that keeps genes with counts per million above 0.5 in at least two libraries keeps 15653 of them.
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For the current analysis, we keep genes that have CPM values above 0.5 in at least two libraries:
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sections[6] "Filtering to remove low counts" paragraph 3
quote
For the current analysis, we keep genes that have CPM values above 0.5 in at least two libraries:
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The filtered libraries are normalised by the trimmed mean of M values, giving one factor per library, from 0.529 for MCL1.LE to 1.370 for MCL1.LA.
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Normalization by trimmed mean of M values (TMM) 17 is performed by using the calcNormFactors function, which returns the DGEList argument with only the norm.factors changed.
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sections[7] "Normalization for composition bias" paragraph 2
quote
Normalization by trimmed mean of M values (TMM) 17 is performed by using the calcNormFactors function, which returns the DGEList argument with only the norm.factors changed.
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The reads are aligned to the GRCm38/mm10 mouse genome with subread 1.4.4, and between 85.3% and 89.7% of the reads are mapped to a unique location.
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Subread version 1.4.4 ( http://subread.sourceforge.net) was used to align the reads to the mouse mm10 genome and featureCounts was used to assign reads to Entrez Genes using RefSeq gene annotation.
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sections[2] "Description of the biological experiment" paragraph 3
quote
Subread version 1.4.4 ( http://subread.sourceforge.net) was used to align the reads to the mouse mm10 genome and featureCounts was used to assign reads to Entrez Genes using RefSeq gene annotation.
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The thresholded result is read for pathway enrichment with edgeR's kegga function, and the fifteen pathways the paper prints include the cell cycle pathway, which it reports as strongly down-regulated upon lactation.
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sections[19] "KEGG pathway analysis" paragraph 2
quote
Another popular annotation database is the Kyoto Encyclopedia of Genes and Genomes (KEGG). Much smaller than GO, this is a curated database of molecular pathways and disease signatures. A KEGG analysis can be done exactly as for GO, but using the kegga function:
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This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq data by providing a complete analysis of an RNA-seq experiment profiling epithelial cell subsets in the mouse mammary gland.
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Transcriptome analysis of luminal and basal cell subpopulations in the lactating versus pregnant mammary gland
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2026-11-03
licence
No licence stated by the publisher.
[8] object · 15 fields
id
code:wehi:edgeRQL.pdf
role
code
format
PDF
media_type
application/pdf
uri
http://bioinf.wehi.edu.au/edgeR/F1000Research2016/edgeRQL.pdf
sha256
sha256:76ea4da65b151b1bb78ba42b0d80c0e864632df0e13219fe968525a43efd2276
bytes
904232
access
open
state
verified
reader
null
reader_status
available
identifier
edgeRQL.pdf
version
null
note
The authors' own file, fetched and hashed on 3 November 2026. The publisher states no licence for the entry.
structure object · 4 fields
repository
WEHI
access_route
the code entry URL
fetched_at
2026-11-03
licence
No licence stated by the publisher.
[9] object · 15 fields
id
reference:mm10
role
reference
format
fasta.gz
media_type
application/gzip
uri
ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001635.6_GRCm38.p4/GCA_000001635.6_GRCm38.p4_genomic.fna.gz
sha256
null
bytes
null
access
open
state
declared
reader
null
reader_status
reader_required
identifier
GCA_000001635.6_GRCm38.p4
version
GRCm38 (Dec 2011)
note
The mouse genome build the paper indexes and aligns to, as the paper names it.
structure object · 4 fields
repository
NCBI
access_route
the NCBI genome FTP path
downloaded
false
licence_read
false
gaps array · 6 items
[0]
asset:data:geo:GSE60450 licence not read
[1]
asset:data:geo:GSE60450 not downloaded
[2]
asset:data:sra:SRP045534 licence not read
[3]
asset:data:sra:SRP045534 not downloaded
[4]
asset:reference:mm10 not downloaded
[5]
data.licence_not_stated_in_the_repository_record
group_sizes object · 6 fields
Basal 18.5 dP
2
Basal 2 dL
2
Basal virgin
2
Luminal 18.5 dP
2
Luminal 2 dL
2
Luminal virgin
2
paper_group_sizes object · 4 fields
sizes object · 6 fields
B.lactating
2
B.pregnant
2
B.virgin
2
L.lactating
2
L.pregnant
2
L.virgin
2
total
12
source
There are therefore six groups of RNA samples, one for each combination of cell type and mouse status. Two biological replicates were collected for each group.
reference_group
B.pregnant
analysis object · 4 fields
state
partial
methods array · 5 items
[0] object · 10 fields
id
method-1
family
read_alignment
specific
Rsubread align to the GRCm38/mm10 reference
label
Read alignment
dsl_operations array · 0 items
missing_operations array · 1 item
[0]
rna_seq_read_alignment
expressible
false
parameters object · 5 fields
aligner
Rsubread 1.4.4, align()
reference
GRCm38/mm10 (Dec 2011), GCA_000001635.6_GRCm38.p4
index
built with buildindex() from the genomic FASTA
reads
100 bp single-end FASTQ, about 30 million per sample
mapped_reads
only reads with a unique mapping location are reported
data_shapes array · 1 item
[0]
FASTQ sequence reads
evidence object · 3 fields
score
1
band
verbatim
quote
Subread version 1.4.4 ( http://subread.sourceforge.net) was used to align the reads to the mouse mm10 genome and featureCounts was used to assign reads to Entrez Genes using RefSeq gene annotation.
[1] object · 10 fields
id
method-2
family
read_quantification
specific
Rsubread featureCounts against the inbuilt RefSeq annotation
label
Gene quantification
dsl_operations array · 0 items
missing_operations array · 1 item
[0]
gene_count_quantification
expressible
false
parameters object · 4 fields
tool
Rsubread featureCounts
annotation
NCBI RefSeq, built in to Rsubread for mm10
identifier
Entrez Gene ID
output
a matrix of read counts per gene per sample
data_shapes array · 2 items
[0]
BAM alignments
[1]
gene annotation
evidence object · 3 fields
score
1
band
verbatim
quote
The read counts for each gene can be quantified using the featureCounts function in Rsubread.
[2] object · 10 fields
id
method-3
family
differential_expression
specific
low-count filtering by counts per million, then TMM normalisation
label
Count filtering and normalisation
dsl_operations array · 1 item
[0]
normalise_counts
missing_operations array · 1 item
[0]
normalise_counts_tmm
expressible
false
parameters object · 5 fields
filter
keep genes with CPM above 0.5 in at least 2 libraries
keep.lib.sizes
false
normalisation
TMM, calcNormFactors()
genes_kept
15653
genes_discarded
10704
data_shapes array · 1 item
[0]
gene-level count matrix
evidence object · 3 fields
score
1
band
verbatim
quote
For the current analysis, we keep genes that have CPM values above 0.5 in at least two libraries:
[3] object · 10 fields
id
method-4
family
differential_expression
specific
edgeR quasi-likelihood F-test with Benjamini-Hochberg false discovery rate, and glmTreat against a fold-change threshold
label
Differential expression
dsl_operations array · 2 items
[0]
differential_expression_fit
[1]
fdr_bh
missing_operations array · 1 item
[0]
differential_expression_quasi_likelihood
expressible
false
parameters object · 5 fields
contrast
B.lactating - B.pregnant
test
QL F-test, glmQLFTest()
false_discovery_rate
Benjamini-Hochberg, 5%
threshold_test
glmTreat(), lfc = log2(1.5) = 0.58
design
one-way layout, six groups, two biological replicates each
data_shapes array · 2 items
[0]
normalised gene-level counts
[1]
group labels
evidence object · 3 fields
score
1
band
verbatim
quote
We will use QL F-tests instead of the more usual likelihood ratio tests (LRT) as they give stricter error rate control by accounting for the uncertainty in dispersion estimation:
[4] object · 10 fields
id
method-5
family
network_analysis
specific
KEGG pathway enrichment with edgeR's kegga on the thresholded result
label
Pathway analysis
dsl_operations array · 1 item
[0]
pathway_enrich
missing_operations array · 0 items
expressible
true
parameters object · 5 fields
organism
Mm
pathways_printed
15
term_truncated_at
34
annotation
KEGG, read from the Internet each time the analysis runs
input
the glmTreat result
data_shapes array · 2 items
[0]
differential expression result
[1]
pathway annotation
evidence object · 3 fields
score
1
band
verbatim
quote
A KEGG analysis can be done exactly as for GO, but using the kegga function:
targets array · 302 items
[0] object · 8 fields
id
target-ql-csn1s2b-logfc
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
6.08
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Csn1s2b, logFC; printed 6.08.
[1] object · 8 fields
id
target-ql-csn1s2b-logcpm
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
10.19
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Csn1s2b, logCPM; printed 10.19.
[2] object · 8 fields
id
target-ql-csn1s2b-f
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
421
unit
F statistic
tolerance
0
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Csn1s2b, F; printed 421.
[3] object · 8 fields
id
target-ql-csn1s2b-pvalue
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
4.78E-11
unit
p-value
tolerance
5.0E-14
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Csn1s2b, PValue; printed 4.78e-11.
[4] object · 8 fields
id
target-ql-csn1s2b-fdr
claim_id
claim-ql-differential-expression
operation
fdr_bh
expected_value
7.48E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Csn1s2b, FDR; printed 7.48e-07.
[5] object · 8 fields
id
target-ql-mrgprf-logfc
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
5.15
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Mrgprf, logFC; printed 5.15.
[6] object · 8 fields
id
target-ql-mrgprf-logcpm
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
2.75
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Mrgprf, logCPM; printed 2.75.
[7] object · 8 fields
id
target-ql-mrgprf-f
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
343
unit
F statistic
tolerance
0
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Mrgprf, F; printed 343.
[8] object · 8 fields
id
target-ql-mrgprf-pvalue
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
1.32E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Mrgprf, PValue; printed 1.32e-10.
[9] object · 8 fields
id
target-ql-mrgprf-fdr
claim_id
claim-ql-differential-expression
operation
fdr_bh
expected_value
7.99E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Mrgprf, FDR; printed 7.99e-07.
[10] object · 8 fields
id
target-ql-myof-logfc
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
2.32
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Myof, logFC; printed 2.32.
[11] object · 8 fields
id
target-ql-myof-logcpm
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
6.45
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Myof, logCPM; printed 6.45.
[12] object · 8 fields
id
target-ql-myof-f
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
322
unit
F statistic
tolerance
0
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Myof, F; printed 322.
[13] object · 8 fields
id
target-ql-myof-pvalue
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
1.97E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Myof, PValue; printed 1.97e-10.
[14] object · 8 fields
id
target-ql-myof-fdr
claim_id
claim-ql-differential-expression
operation
fdr_bh
expected_value
7.99E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Myof, FDR; printed 7.99e-07.
[15] object · 8 fields
id
target-ql-atp2b4-logfc
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
2.14
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Atp2b4, logFC; printed 2.14.
[16] object · 8 fields
id
target-ql-atp2b4-logcpm
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
6.15
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Atp2b4, logCPM; printed 6.15.
[17] object · 8 fields
id
target-ql-atp2b4-f
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
320
unit
F statistic
tolerance
0
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Atp2b4, F; printed 320.
[18] object · 8 fields
id
target-ql-atp2b4-pvalue
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
2.04E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Atp2b4, PValue; printed 2.04e-10.
[19] object · 8 fields
id
target-ql-atp2b4-fdr
claim_id
claim-ql-differential-expression
operation
fdr_bh
expected_value
7.99E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Atp2b4, FDR; printed 7.99e-07.
[20] object · 8 fields
id
target-ql-muc4-logfc
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
-7.17
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Muc4, logFC; printed -7.17.
[21] object · 8 fields
id
target-ql-muc4-logcpm
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
6.06
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Muc4, logCPM; printed 6.06.
[22] object · 8 fields
id
target-ql-muc4-f
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
308
unit
F statistic
tolerance
0
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Muc4, F; printed 308.
[23] object · 8 fields
id
target-ql-muc4-pvalue
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
2.6E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Muc4, PValue; printed 2.60e-10.
[24] object · 8 fields
id
target-ql-muc4-fdr
claim_id
claim-ql-differential-expression
operation
fdr_bh
expected_value
8.15E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Muc4, FDR; printed 8.15e-07.
[25] object · 8 fields
id
target-ql-micall2-logfc
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
-2.25
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Micall2, logFC; printed -2.25.
[26] object · 8 fields
id
target-ql-micall2-logcpm
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
5.19
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Micall2, logCPM; printed 5.19.
[27] object · 8 fields
id
target-ql-micall2-f
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
282
unit
F statistic
tolerance
0
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Micall2, F; printed 282.
[28] object · 8 fields
id
target-ql-micall2-pvalue
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
4.41E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Micall2, PValue; printed 4.41e-10.
[29] object · 8 fields
id
target-ql-micall2-fdr
claim_id
claim-ql-differential-expression
operation
fdr_bh
expected_value
1.15E-6
unit
false discovery rate
tolerance
5.0E-9
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Micall2, FDR; printed 1.15e-06.
[30] object · 8 fields
id
target-ql-wif1-logfc
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
-1.82
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Wif1, logFC; printed -1.82.
[31] object · 8 fields
id
target-ql-wif1-logcpm
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
6.77
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Wif1, logCPM; printed 6.77.
[32] object · 8 fields
id
target-ql-wif1-f
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
261
unit
F statistic
tolerance
0
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Wif1, F; printed 261.
[33] object · 8 fields
id
target-ql-wif1-pvalue
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
7.13E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Wif1, PValue; printed 7.13e-10.
[34] object · 8 fields
id
target-ql-wif1-fdr
claim_id
claim-ql-differential-expression
operation
fdr_bh
expected_value
1.6E-6
unit
false discovery rate
tolerance
5.0E-9
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Wif1, FDR; printed 1.60e-06.
[35] object · 8 fields
id
target-ql-cldn4-logfc
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
-5.32
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Cldn4, logFC; printed -5.32.
[36] object · 8 fields
id
target-ql-cldn4-logcpm
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
9.87
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Cldn4, logCPM; printed 9.87.
[37] object · 8 fields
id
target-ql-cldn4-f
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
298
unit
F statistic
tolerance
0
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Cldn4, F; printed 298.
[38] object · 8 fields
id
target-ql-cldn4-pvalue
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
9.12E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Cldn4, PValue; printed 9.12e-10.
[39] object · 8 fields
id
target-ql-cldn4-fdr
claim_id
claim-ql-differential-expression
operation
fdr_bh
expected_value
1.74E-6
unit
false discovery rate
tolerance
5.0E-9
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Cldn4, FDR; printed 1.74e-06.
[40] object · 8 fields
id
target-ql-tnni2-logfc
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
5.75
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Tnni2, logFC; printed 5.75.
[41] object · 8 fields
id
target-ql-tnni2-logcpm
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
3.86
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Tnni2, logCPM; printed 3.86.
[42] object · 8 fields
id
target-ql-tnni2-f
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
313
unit
F statistic
tolerance
0
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Tnni2, F; printed 313.
[43] object · 8 fields
id
target-ql-tnni2-pvalue
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
1.0E-9
unit
p-value
tolerance
5.0E-12
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Tnni2, PValue; printed 1.00e-09.
[44] object · 8 fields
id
target-ql-tnni2-fdr
claim_id
claim-ql-differential-expression
operation
fdr_bh
expected_value
1.74E-6
unit
false discovery rate
tolerance
5.0E-9
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Tnni2, FDR; printed 1.74e-06.
[45] object · 8 fields
id
target-ql-creb5-logfc
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
2.57
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Creb5, logFC; printed 2.57.
[46] object · 8 fields
id
target-ql-creb5-logcpm
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
4.87
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Creb5, logCPM; printed 4.87.
[47] object · 8 fields
id
target-ql-creb5-f
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
240
unit
F statistic
tolerance
0
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Creb5, F; printed 240.
[48] object · 8 fields
id
target-ql-creb5-pvalue
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
1.17E-9
unit
p-value
tolerance
5.0E-12
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Creb5, PValue; printed 1.17e-09.
[49] object · 8 fields
id
target-ql-creb5-fdr
claim_id
claim-ql-differential-expression
operation
fdr_bh
expected_value
1.83E-6
unit
false discovery rate
tolerance
5.0E-9
state
complete
note
Section 12, the topTags printout of the quasi-likelihood F-test: Creb5, FDR; printed 1.83e-06.
[50] object · 8 fields
id
target-glmtreat-csn1s2b-logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
6.08
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Csn1s2b, logFC; printed 6.08.
[51] object · 8 fields
id
target-glmtreat-csn1s2b-unshrunk.logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
6.09
unit
log2 fold change, unshrunk (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Csn1s2b, unshrunk.logFC; printed 6.09.
[52] object · 8 fields
id
target-glmtreat-csn1s2b-logcpm
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
10.19
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Csn1s2b, logCPM; printed 10.19.
[53] object · 8 fields
id
target-glmtreat-csn1s2b-pvalue
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
5.94E-11
unit
p-value
tolerance
5.0E-14
state
complete
note
Section 13, the topTags printout of the glmTreat test: Csn1s2b, PValue; printed 5.94e-11.
[54] object · 8 fields
id
target-glmtreat-csn1s2b-fdr
claim_id
claim-glmtreat-threshold
operation
fdr_bh
expected_value
9.3E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 13, the topTags printout of the glmTreat test: Csn1s2b, FDR; printed 9.30e-07.
[55] object · 8 fields
id
target-glmtreat-mrgprf-logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
5.15
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Mrgprf, logFC; printed 5.15.
[56] object · 8 fields
id
target-glmtreat-mrgprf-unshrunk.logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
5.15
unit
log2 fold change, unshrunk (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Mrgprf, unshrunk.logFC; printed 5.15.
[57] object · 8 fields
id
target-glmtreat-mrgprf-logcpm
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
2.75
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Mrgprf, logCPM; printed 2.75.
[58] object · 8 fields
id
target-glmtreat-mrgprf-pvalue
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
1.77E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 13, the topTags printout of the glmTreat test: Mrgprf, PValue; printed 1.77e-10.
[59] object · 8 fields
id
target-glmtreat-mrgprf-fdr
claim_id
claim-glmtreat-threshold
operation
fdr_bh
expected_value
1.38E-6
unit
false discovery rate
tolerance
5.0E-9
state
complete
note
Section 13, the topTags printout of the glmTreat test: Mrgprf, FDR; printed 1.38e-06.
[60] object · 8 fields
id
target-glmtreat-muc4-logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
-7.17
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Muc4, logFC; printed -7.17.
[61] object · 8 fields
id
target-glmtreat-muc4-unshrunk.logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
-7.34
unit
log2 fold change, unshrunk (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Muc4, unshrunk.logFC; printed -7.34.
[62] object · 8 fields
id
target-glmtreat-muc4-logcpm
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
6.06
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Muc4, logCPM; printed 6.06.
[63] object · 8 fields
id
target-glmtreat-muc4-pvalue
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
3.98E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 13, the topTags printout of the glmTreat test: Muc4, PValue; printed 3.98e-10.
[64] object · 8 fields
id
target-glmtreat-muc4-fdr
claim_id
claim-glmtreat-threshold
operation
fdr_bh
expected_value
2.07E-6
unit
false discovery rate
tolerance
5.0E-9
state
complete
note
Section 13, the topTags printout of the glmTreat test: Muc4, FDR; printed 2.07e-06.
[65] object · 8 fields
id
target-glmtreat-myof-logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
2.32
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Myof, logFC; printed 2.32.
[66] object · 8 fields
id
target-glmtreat-myof-unshrunk.logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
2.32
unit
log2 fold change, unshrunk (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Myof, unshrunk.logFC; printed 2.32.
[67] object · 8 fields
id
target-glmtreat-myof-logcpm
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
6.45
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Myof, logCPM; printed 6.45.
[68] object · 8 fields
id
target-glmtreat-myof-pvalue
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
7.82E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 13, the topTags printout of the glmTreat test: Myof, PValue; printed 7.82e-10.
[69] object · 8 fields
id
target-glmtreat-myof-fdr
claim_id
claim-glmtreat-threshold
operation
fdr_bh
expected_value
2.69E-6
unit
false discovery rate
tolerance
5.0E-9
state
complete
note
Section 13, the topTags printout of the glmTreat test: Myof, FDR; printed 2.69e-06.
[70] object · 8 fields
id
target-glmtreat-atp2b4-logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
2.14
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Atp2b4, logFC; printed 2.14.
[71] object · 8 fields
id
target-glmtreat-atp2b4-unshrunk.logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
2.14
unit
log2 fold change, unshrunk (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Atp2b4, unshrunk.logFC; printed 2.14.
[72] object · 8 fields
id
target-glmtreat-atp2b4-logcpm
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
6.15
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Atp2b4, logCPM; printed 6.15.
[73] object · 8 fields
id
target-glmtreat-atp2b4-pvalue
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
1.01E-9
unit
p-value
tolerance
5.0E-12
state
complete
note
Section 13, the topTags printout of the glmTreat test: Atp2b4, PValue; printed 1.01e-09.
[74] object · 8 fields
id
target-glmtreat-atp2b4-fdr
claim_id
claim-glmtreat-threshold
operation
fdr_bh
expected_value
2.69E-6
unit
false discovery rate
tolerance
5.0E-9
state
complete
note
Section 13, the topTags printout of the glmTreat test: Atp2b4, FDR; printed 2.69e-06.
[75] object · 8 fields
id
target-glmtreat-cldn4-logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
-5.32
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Cldn4, logFC; printed -5.32.
[76] object · 8 fields
id
target-glmtreat-cldn4-unshrunk.logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
-5.32
unit
log2 fold change, unshrunk (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Cldn4, unshrunk.logFC; printed -5.32.
[77] object · 8 fields
id
target-glmtreat-cldn4-logcpm
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
9.87
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Cldn4, logCPM; printed 9.87.
[78] object · 8 fields
id
target-glmtreat-cldn4-pvalue
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
1.14E-9
unit
p-value
tolerance
5.0E-12
state
complete
note
Section 13, the topTags printout of the glmTreat test: Cldn4, PValue; printed 1.14e-09.
[79] object · 8 fields
id
target-glmtreat-cldn4-fdr
claim_id
claim-glmtreat-threshold
operation
fdr_bh
expected_value
2.69E-6
unit
false discovery rate
tolerance
5.0E-9
state
complete
note
Section 13, the topTags printout of the glmTreat test: Cldn4, FDR; printed 2.69e-06.
[80] object · 8 fields
id
target-glmtreat-tnni2-logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
5.75
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Tnni2, logFC; printed 5.75.
[81] object · 8 fields
id
target-glmtreat-tnni2-unshrunk.logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
5.76
unit
log2 fold change, unshrunk (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Tnni2, unshrunk.logFC; printed 5.76.
[82] object · 8 fields
id
target-glmtreat-tnni2-logcpm
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
3.86
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Tnni2, logCPM; printed 3.86.
[83] object · 8 fields
id
target-glmtreat-tnni2-pvalue
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
1.2E-9
unit
p-value
tolerance
5.0E-12
state
complete
note
Section 13, the topTags printout of the glmTreat test: Tnni2, PValue; printed 1.20e-09.
[84] object · 8 fields
id
target-glmtreat-tnni2-fdr
claim_id
claim-glmtreat-threshold
operation
fdr_bh
expected_value
2.69E-6
unit
false discovery rate
tolerance
5.0E-9
state
complete
note
Section 13, the topTags printout of the glmTreat test: Tnni2, FDR; printed 2.69e-06.
[85] object · 8 fields
id
target-glmtreat-micall2-logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
-2.25
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Micall2, logFC; printed -2.25.
[86] object · 8 fields
id
target-glmtreat-micall2-unshrunk.logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
-2.25
unit
log2 fold change, unshrunk (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Micall2, unshrunk.logFC; printed -2.25.
[87] object · 8 fields
id
target-glmtreat-micall2-logcpm
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
5.19
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Micall2, logCPM; printed 5.19.
[88] object · 8 fields
id
target-glmtreat-micall2-pvalue
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
1.9E-9
unit
p-value
tolerance
5.0E-12
state
complete
note
Section 13, the topTags printout of the glmTreat test: Micall2, PValue; printed 1.90e-09.
[89] object · 8 fields
id
target-glmtreat-micall2-fdr
claim_id
claim-glmtreat-threshold
operation
fdr_bh
expected_value
3.71E-6
unit
false discovery rate
tolerance
5.0E-9
state
complete
note
Section 13, the topTags printout of the glmTreat test: Micall2, FDR; printed 3.71e-06.
[90] object · 8 fields
id
target-glmtreat-creb5-logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
2.57
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Creb5, logFC; printed 2.57.
[91] object · 8 fields
id
target-glmtreat-creb5-unshrunk.logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
2.57
unit
log2 fold change, unshrunk (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Creb5, unshrunk.logFC; printed 2.57.
[92] object · 8 fields
id
target-glmtreat-creb5-logcpm
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
4.87
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Creb5, logCPM; printed 4.87.
[93] object · 8 fields
id
target-glmtreat-creb5-pvalue
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
3.55E-9
unit
p-value
tolerance
5.0E-12
state
complete
note
Section 13, the topTags printout of the glmTreat test: Creb5, PValue; printed 3.55e-09.
[94] object · 8 fields
id
target-glmtreat-creb5-fdr
claim_id
claim-glmtreat-threshold
operation
fdr_bh
expected_value
6.18E-6
unit
false discovery rate
tolerance
5.0E-9
state
complete
note
Section 13, the topTags printout of the glmTreat test: Creb5, FDR; printed 6.18e-06.
[95] object · 8 fields
id
target-glmtreat-igfbp6-logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
2.87
unit
log2 fold change (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Igfbp6, logFC; printed 2.87.
[96] object · 8 fields
id
target-glmtreat-igfbp6-unshrunk.logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
2.87
unit
log2 fold change, unshrunk (basal lactating - basal pregnant)
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Igfbp6, unshrunk.logFC; printed 2.87.
[97] object · 8 fields
id
target-glmtreat-igfbp6-logcpm
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
3.68
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 13, the topTags printout of the glmTreat test: Igfbp6, logCPM; printed 3.68.
[98] object · 8 fields
id
target-glmtreat-igfbp6-pvalue
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
4.6E-9
unit
p-value
tolerance
5.0E-12
state
complete
note
Section 13, the topTags printout of the glmTreat test: Igfbp6, PValue; printed 4.60e-09.
[99] object · 8 fields
id
target-glmtreat-igfbp6-fdr
claim_id
claim-glmtreat-threshold
operation
fdr_bh
expected_value
7.2E-6
unit
false discovery rate
tolerance
5.0E-9
state
complete
note
Section 13, the topTags printout of the glmTreat test: Igfbp6, FDR; printed 7.20e-06.
[100] object · 8 fields
id
target-interaction-ppl-logfc
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
-4.62
unit
log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Ppl, logFC; printed -4.62.
[101] object · 8 fields
id
target-interaction-ppl-logcpm
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
6.96
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Ppl, logCPM; printed 6.96.
[102] object · 8 fields
id
target-interaction-ppl-f
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
524
unit
F statistic
tolerance
0
state
complete
note
Section 16, the topTags printout of the interaction contrast: Ppl, F; printed 524.
[103] object · 8 fields
id
target-interaction-ppl-pvalue
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
9.55E-12
unit
p-value
tolerance
5.0E-15
state
complete
note
Section 16, the topTags printout of the interaction contrast: Ppl, PValue; printed 9.55e-12.
[104] object · 8 fields
id
target-interaction-ppl-fdr
claim_id
claim-interaction
operation
fdr_bh
expected_value
1.49E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 16, the topTags printout of the interaction contrast: Ppl, FDR; printed 1.49e-07.
[105] object · 8 fields
id
target-interaction-creb5-logfc
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
-5.61
unit
log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Creb5, logFC; printed -5.61.
[106] object · 8 fields
id
target-interaction-creb5-logcpm
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
4.87
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Creb5, logCPM; printed 4.87.
[107] object · 8 fields
id
target-interaction-creb5-f
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
438
unit
F statistic
tolerance
0
state
complete
note
Section 16, the topTags printout of the interaction contrast: Creb5, F; printed 438.
[108] object · 8 fields
id
target-interaction-creb5-pvalue
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
2.91E-11
unit
p-value
tolerance
5.0E-14
state
complete
note
Section 16, the topTags printout of the interaction contrast: Creb5, PValue; printed 2.91e-11.
[109] object · 8 fields
id
target-interaction-creb5-fdr
claim_id
claim-interaction
operation
fdr_bh
expected_value
2.13E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 16, the topTags printout of the interaction contrast: Creb5, FDR; printed 2.13e-07.
[110] object · 8 fields
id
target-interaction-slc1a3-logfc
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
5.03
unit
log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Slc1a3, logFC; printed 5.03.
[111] object · 8 fields
id
target-interaction-slc1a3-logcpm
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
3.65
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Slc1a3, logCPM; printed 3.65.
[112] object · 8 fields
id
target-interaction-slc1a3-f
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
415
unit
F statistic
tolerance
0
state
complete
note
Section 16, the topTags printout of the interaction contrast: Slc1a3, F; printed 415.
[113] object · 8 fields
id
target-interaction-slc1a3-pvalue
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
4.09E-11
unit
p-value
tolerance
5.0E-14
state
complete
note
Section 16, the topTags printout of the interaction contrast: Slc1a3, PValue; printed 4.09e-11.
[114] object · 8 fields
id
target-interaction-slc1a3-fdr
claim_id
claim-interaction
operation
fdr_bh
expected_value
2.13E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 16, the topTags printout of the interaction contrast: Slc1a3, FDR; printed 2.13e-07.
[115] object · 8 fields
id
target-interaction-bc006965-logfc
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
-3.88
unit
log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: BC006965, logFC; printed -3.88.
[116] object · 8 fields
id
target-interaction-bc006965-logcpm
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
4.68
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: BC006965, logCPM; printed 4.68.
[117] object · 8 fields
id
target-interaction-bc006965-f
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
372
unit
F statistic
tolerance
0
state
complete
note
Section 16, the topTags printout of the interaction contrast: BC006965, F; printed 372.
[118] object · 8 fields
id
target-interaction-bc006965-pvalue
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
8.11E-11
unit
p-value
tolerance
5.0E-14
state
complete
note
Section 16, the topTags printout of the interaction contrast: BC006965, PValue; printed 8.11e-11.
[119] object · 8 fields
id
target-interaction-bc006965-fdr
claim_id
claim-interaction
operation
fdr_bh
expected_value
2.86E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 16, the topTags printout of the interaction contrast: BC006965, FDR; printed 2.86e-07.
[120] object · 8 fields
id
target-interaction-ggt1-logfc
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
3.17
unit
log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Ggt1, logFC; printed 3.17.
[121] object · 8 fields
id
target-interaction-ggt1-logcpm
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
6.38
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Ggt1, logCPM; printed 6.38.
[122] object · 8 fields
id
target-interaction-ggt1-f
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
357
unit
F statistic
tolerance
0
state
complete
note
Section 16, the topTags printout of the interaction contrast: Ggt1, F; printed 357.
[123] object · 8 fields
id
target-interaction-ggt1-pvalue
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
1.04E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 16, the topTags printout of the interaction contrast: Ggt1, PValue; printed 1.04e-10.
[124] object · 8 fields
id
target-interaction-ggt1-fdr
claim_id
claim-interaction
operation
fdr_bh
expected_value
2.86E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 16, the topTags printout of the interaction contrast: Ggt1, FDR; printed 2.86e-07.
[125] object · 8 fields
id
target-interaction-slc25a1-logfc
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
3.47
unit
log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Slc25a1, logFC; printed 3.47.
[126] object · 8 fields
id
target-interaction-slc25a1-logcpm
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
7.5
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Slc25a1, logCPM; printed 7.50.
[127] object · 8 fields
id
target-interaction-slc25a1-f
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
354
unit
F statistic
tolerance
0
state
complete
note
Section 16, the topTags printout of the interaction contrast: Slc25a1, F; printed 354.
[128] object · 8 fields
id
target-interaction-slc25a1-pvalue
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
1.1E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 16, the topTags printout of the interaction contrast: Slc25a1, PValue; printed 1.10e-10.
[129] object · 8 fields
id
target-interaction-slc25a1-fdr
claim_id
claim-interaction
operation
fdr_bh
expected_value
2.86E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 16, the topTags printout of the interaction contrast: Slc25a1, FDR; printed 2.86e-07.
[130] object · 8 fields
id
target-interaction-sardh-logfc
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
2.92
unit
log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Sardh, logFC; printed 2.92.
[131] object · 8 fields
id
target-interaction-sardh-logcpm
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
5.11
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Sardh, logCPM; printed 5.11.
[132] object · 8 fields
id
target-interaction-sardh-f
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
342
unit
F statistic
tolerance
0
state
complete
note
Section 16, the topTags printout of the interaction contrast: Sardh, F; printed 342.
[133] object · 8 fields
id
target-interaction-sardh-pvalue
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
1.36E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 16, the topTags printout of the interaction contrast: Sardh, PValue; printed 1.36e-10.
[134] object · 8 fields
id
target-interaction-sardh-fdr
claim_id
claim-interaction
operation
fdr_bh
expected_value
3.04E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 16, the topTags printout of the interaction contrast: Sardh, FDR; printed 3.04e-07.
[135] object · 8 fields
id
target-interaction-rbp1-logfc
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
-4.4
unit
log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Rbp1, logFC; printed -4.40.
[136] object · 8 fields
id
target-interaction-rbp1-logcpm
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
6.83
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Rbp1, logCPM; printed 6.83.
[137] object · 8 fields
id
target-interaction-rbp1-f
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
337
unit
F statistic
tolerance
0
state
complete
note
Section 16, the topTags printout of the interaction contrast: Rbp1, F; printed 337.
[138] object · 8 fields
id
target-interaction-rbp1-pvalue
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
1.63E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 16, the topTags printout of the interaction contrast: Rbp1, PValue; printed 1.63e-10.
[139] object · 8 fields
id
target-interaction-rbp1-fdr
claim_id
claim-interaction
operation
fdr_bh
expected_value
3.18E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 16, the topTags printout of the interaction contrast: Rbp1, FDR; printed 3.18e-07.
[140] object · 8 fields
id
target-interaction-slc39a8-logfc
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
6.19
unit
log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Slc39a8, logFC; printed 6.19.
[141] object · 8 fields
id
target-interaction-slc39a8-logcpm
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
5.07
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: Slc39a8, logCPM; printed 5.07.
[142] object · 8 fields
id
target-interaction-slc39a8-f
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
376
unit
F statistic
tolerance
0
state
complete
note
Section 16, the topTags printout of the interaction contrast: Slc39a8, F; printed 376.
[143] object · 8 fields
id
target-interaction-slc39a8-pvalue
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
1.83E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 16, the topTags printout of the interaction contrast: Slc39a8, PValue; printed 1.83e-10.
[144] object · 8 fields
id
target-interaction-slc39a8-fdr
claim_id
claim-interaction
operation
fdr_bh
expected_value
3.18E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 16, the topTags printout of the interaction contrast: Slc39a8, FDR; printed 3.18e-07.
[145] object · 8 fields
id
target-interaction-f2rl1-logfc
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
-3.92
unit
log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: F2rl1, logFC; printed -3.92.
[146] object · 8 fields
id
target-interaction-f2rl1-logcpm
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
5.61
unit
log2 counts per million
tolerance
0.005
state
complete
note
Section 16, the topTags printout of the interaction contrast: F2rl1, logCPM; printed 5.61.
[147] object · 8 fields
id
target-interaction-f2rl1-f
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
302
unit
F statistic
tolerance
0
state
complete
note
Section 16, the topTags printout of the interaction contrast: F2rl1, F; printed 302.
[148] object · 8 fields
id
target-interaction-f2rl1-pvalue
claim_id
claim-interaction
operation
differential_expression_fit
expected_value
2.93E-10
unit
p-value
tolerance
5.0E-13
state
complete
note
Section 16, the topTags printout of the interaction contrast: F2rl1, PValue; printed 2.93e-10.
[149] object · 8 fields
id
target-interaction-f2rl1-fdr
claim_id
claim-interaction
operation
fdr_bh
expected_value
4.2E-7
unit
false discovery rate
tolerance
5.0E-10
state
complete
note
Section 16, the topTags printout of the interaction contrast: F2rl1, FDR; printed 4.20e-07.
[150] object · 8 fields
id
target-counts-genes
claim_id
claim-counts
operation
normalise_counts
expected_value
27179
unit
genes in the count matrix
tolerance
0
state
complete
note
Section 4: dim(GenewiseCounts) is 27179 genes by 13 columns, the gene length column and the twelve libraries.
[151] object · 8 fields
id
target-counts-libraries
claim_id
claim-counts
operation
normalise_counts
expected_value
12
unit
libraries in the count matrix
tolerance
0
state
complete
note
Section 4: the count matrix carries one column per library, twelve of them, and one column of gene lengths.
[152] object · 8 fields
id
target-filter-kept
claim_id
claim-counts
operation
normalise_counts
expected_value
15653
unit
genes kept by the filter
tolerance
0
state
complete
note
Section 6: the rule is CPM above 0.5 in at least two libraries, and it keeps 15653 genes.
[153] object · 8 fields
id
target-filter-discarded
claim_id
claim-counts
operation
normalise_counts
expected_value
10704
unit
genes discarded by the filter
tolerance
0
state
complete
note
Section 6: the same rule discards 10704 genes.
[154] object · 8 fields
id
target-ql-de-down
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
2757
unit
genes called down
tolerance
0
state
complete
note
Section 12: summary(decideTestsDGE) calls 2757 genes down.
[155] object · 8 fields
id
target-ql-de-none
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
10408
unit
genes called none
tolerance
0
state
complete
note
Section 12: summary(decideTestsDGE) calls 10408 genes none.
[156] object · 8 fields
id
target-ql-de-up
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
2488
unit
genes called up
tolerance
0
state
complete
note
Section 12: summary(decideTestsDGE) calls 2488 genes up.
[157] object · 8 fields
id
target-glmtreat-de-down
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
723
unit
genes called down
tolerance
0
state
complete
note
Section 13: summary(decideTestsDGE) calls 723 genes down.
[158] object · 8 fields
id
target-glmtreat-de-none
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
14530
unit
genes called none
tolerance
0
state
complete
note
Section 13: summary(decideTestsDGE) calls 14530 genes none.
[159] object · 8 fields
id
target-glmtreat-de-up
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
400
unit
genes called up
tolerance
0
state
complete
note
Section 13: summary(decideTestsDGE) calls 400 genes up.
[160] object · 8 fields
id
target-fdr-threshold
claim_id
claim-ql-differential-expression
operation
fdr_bh
expected_value
0.05
unit
exclusive false-discovery-rate threshold
tolerance
0
state
complete
note
Section 12: the false discovery rate is controlled at 5% by the Benjamini-Hochberg method.
[161] object · 8 fields
id
target-ql-de-count-prose
claim_id
claim-ql-differential-expression
operation
differential_expression_fit
expected_value
5000
unit
genes (the paper states more than this)
tolerance
null
state
partial
note
Section 12: the paper states there are in fact more than 5000 differentially expressed genes in this comparison. The count is a lower bound, not a value.
[162] object · 8 fields
id
target-glmtreat-lfc-threshold
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
1.5
unit
fold-change threshold
tolerance
0
state
complete
note
Section 13: glmTreat is called with lfc = log2(1.5), so the test asks whether the fold changes are significantly greater than 1.5.
[163] object · 8 fields
id
target-glmtreat-log2-threshold
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
0.58
unit
log2 fold-change threshold
tolerance
0.005
state
complete
note
Section 13: the paper states the threshold value of log 2(1.5) = 0.58.
[164] object · 8 fields
id
target-glmtreat-de-count-prose
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
1100
unit
genes (the paper states about this many)
tolerance
null
state
partial
note
Section 13: about 1100 genes are detected as differentially expressed with a fold change significantly above 1.5 at a false discovery rate of 5%. The count is approximate.
[165] object · 8 fields
id
target-glmtreat-min-logfc
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
0.8
unit
log2 fold change, lower bound on the significant genes
tolerance
null
state
partial
note
Section 13: all the statistically significant expression changes have logFC greater than 0.8. The value is a bound, not an estimate.
[166] object · 8 fields
id
target-glmtreat-share-above-0.9
claim_id
claim-glmtreat-threshold
operation
differential_expression_fit
expected_value
97
unit
percent of the significant genes with logFC above 0.9
tolerance
null
state
partial
note
Section 13: almost all (97%) of the significant genes have logFC greater than 0.9. The value is a share read off the paper's own summary.
[167] object · 8 fields
id
target-libsize-mcl1.dg
claim_id
claim-normalisation
operation
normalise_counts
expected_value
23139638
unit
reads in the library after filtering
tolerance
0
state
complete
note
Section 7: MCL1.DG, group B.virgin, lib.size 23139638 after the filter and the TMM normalisation.
[168] object · 8 fields
id
target-normfactor-mcl1.dg
claim_id
claim-normalisation
operation
normalise_counts
expected_value
1.235
unit
TMM normalisation factor
tolerance
0.0005
state
complete
note
Section 7: MCL1.DG, group B.virgin, norm.factors 1.235.
[169] object · 8 fields
id
target-libsize-mcl1.dh
claim_id
claim-normalisation
operation
normalise_counts
expected_value
21689576
unit
reads in the library after filtering
tolerance
0
state
complete
note
Section 7: MCL1.DH, group B.virgin, lib.size 21689576 after the filter and the TMM normalisation.
[170] object · 8 fields
id
target-normfactor-mcl1.dh
claim_id
claim-normalisation
operation
normalise_counts
expected_value
1.213
unit
TMM normalisation factor
tolerance
0.0005
state
complete
note
Section 7: MCL1.DH, group B.virgin, norm.factors 1.213.
[171] object · 8 fields
id
target-libsize-mcl1.di
claim_id
claim-normalisation
operation
normalise_counts
expected_value
23976634
unit
reads in the library after filtering
tolerance
0
state
complete
note
Section 7: MCL1.DI, group B.pregnant, lib.size 23976634 after the filter and the TMM normalisation.
[172] object · 8 fields
id
target-normfactor-mcl1.di
claim_id
claim-normalisation
operation
normalise_counts
expected_value
1.126
unit
TMM normalisation factor
tolerance
0.0005
state
complete
note
Section 7: MCL1.DI, group B.pregnant, norm.factors 1.126.
[173] object · 8 fields
id
target-libsize-mcl1.dj
claim_id
claim-normalisation
operation
normalise_counts
expected_value
22546909
unit
reads in the library after filtering
tolerance
0
state
complete
note
Section 7: MCL1.DJ, group B.pregnant, lib.size 22546909 after the filter and the TMM normalisation.
[174] object · 8 fields
id
target-normfactor-mcl1.dj
claim_id
claim-normalisation
operation
normalise_counts
expected_value
1.069
unit
TMM normalisation factor
tolerance
0.0005
state
complete
note
Section 7: MCL1.DJ, group B.pregnant, norm.factors 1.069.
[175] object · 8 fields
id
target-libsize-mcl1.dk
claim_id
claim-normalisation
operation
normalise_counts
expected_value
21422164
unit
reads in the library after filtering
tolerance
0
state
complete
note
Section 7: MCL1.DK, group B.lactating, lib.size 21422164 after the filter and the TMM normalisation.
[176] object · 8 fields
id
target-normfactor-mcl1.dk
claim_id
claim-normalisation
operation
normalise_counts
expected_value
1.036
unit
TMM normalisation factor
tolerance
0.0005
state
complete
note
Section 7: MCL1.DK, group B.lactating, norm.factors 1.036.
[177] object · 8 fields
id
target-libsize-mcl1.dl
claim_id
claim-normalisation
operation
normalise_counts
expected_value
19918278
unit
reads in the library after filtering
tolerance
0
state
complete
note
Section 7: MCL1.DL, group B.lactating, lib.size 19918278 after the filter and the TMM normalisation.
[178] object · 8 fields
id
target-normfactor-mcl1.dl
claim_id
claim-normalisation
operation
normalise_counts
expected_value
1.087
unit
TMM normalisation factor
tolerance
0.0005
state
complete
note
Section 7: MCL1.DL, group B.lactating, norm.factors 1.087.
[179] object · 8 fields
id
target-libsize-mcl1.la
claim_id
claim-normalisation
operation
normalise_counts
expected_value
20276400
unit
reads in the library after filtering
tolerance
0
state
complete
note
Section 7: MCL1.LA, group L.virgin, lib.size 20276400 after the filter and the TMM normalisation.
[180] object · 8 fields
id
target-normfactor-mcl1.la
claim_id
claim-normalisation
operation
normalise_counts
expected_value
1.37
unit
TMM normalisation factor
tolerance
0.0005
state
complete
note
Section 7: MCL1.LA, group L.virgin, norm.factors 1.370.
[181] object · 8 fields
id
target-libsize-mcl1.lb
claim_id
claim-normalisation
operation
normalise_counts
expected_value
21571124
unit
reads in the library after filtering
tolerance
0
state
complete
note
Section 7: MCL1.LB, group L.virgin, lib.size 21571124 after the filter and the TMM normalisation.
[182] object · 8 fields
id
target-normfactor-mcl1.lb
claim_id
claim-normalisation
operation
normalise_counts
expected_value
1.368
unit
TMM normalisation factor
tolerance
0.0005
state
complete
note
Section 7: MCL1.LB, group L.virgin, norm.factors 1.368.
[183] object · 8 fields
id
target-libsize-mcl1.lc
claim_id
claim-normalisation
operation
normalise_counts
expected_value
22120647
unit
reads in the library after filtering
tolerance
0
state
complete
note
Section 7: MCL1.LC, group L.pregnant, lib.size 22120647 after the filter and the TMM normalisation.
[184] object · 8 fields
id
target-normfactor-mcl1.lc
claim_id
claim-normalisation
operation
normalise_counts
expected_value
1.006
unit
TMM normalisation factor
tolerance
0.0005
state
complete
note
Section 7: MCL1.LC, group L.pregnant, norm.factors 1.006.
[185] object · 8 fields
id
target-libsize-mcl1.ld
claim_id
claim-normalisation
operation
normalise_counts
expected_value
21879947
unit
reads in the library after filtering
tolerance
0
state
complete
note
Section 7: MCL1.LD, group L.pregnant, lib.size 21879947 after the filter and the TMM normalisation.
[186] object · 8 fields
id
target-normfactor-mcl1.ld
claim_id
claim-normalisation
operation
normalise_counts
expected_value
0.924
unit
TMM normalisation factor
tolerance
0.0005
state
complete
note
Section 7: MCL1.LD, group L.pregnant, norm.factors 0.924.
[187] object · 8 fields
id
target-libsize-mcl1.le
claim_id
claim-normalisation
operation
normalise_counts
expected_value
24660577
unit
reads in the library after filtering
tolerance
0
state
complete
note
Section 7: MCL1.LE, group L.lactating, lib.size 24660577 after the filter and the TMM normalisation.
[188] object · 8 fields
id
target-normfactor-mcl1.le
claim_id
claim-normalisation
operation
normalise_counts
expected_value
0.529
unit
TMM normalisation factor
tolerance
0.0005
state
complete
note
Section 7: MCL1.LE, group L.lactating, norm.factors 0.529.
[189] object · 8 fields
id
target-libsize-mcl1.lf
claim_id
claim-normalisation
operation
normalise_counts
expected_value
24602860
unit
reads in the library after filtering
tolerance
0
state
complete
note
Section 7: MCL1.LF, group L.lactating, lib.size 24602860 after the filter and the TMM normalisation.
[190] object · 8 fields
id
target-normfactor-mcl1.lf
claim_id
claim-normalisation
operation
normalise_counts
expected_value
0.535
unit
TMM normalisation factor
tolerance
0.0005
state
complete
note
Section 7: MCL1.LF, group L.lactating, norm.factors 0.535.
[191] object · 8 fields
id
target-mapping-srr1552450-num_total
claim_id
claim-alignment
operation
null
expected_value
30109290
unit
reads in the library
tolerance
null
state
partial
note
Section 27: SRR1552450, num total 30109290. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[192] object · 8 fields
id
target-mapping-srr1552450-num_mapped
claim_id
claim-alignment
operation
null
expected_value
26577308
unit
reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552450, num mapped 26577308. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[193] object · 8 fields
id
target-mapping-srr1552450-prop
claim_id
claim-alignment
operation
null
expected_value
0.883
unit
proportion of reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552450, PropMapped 0.883. The paper states that the proportion of mapped reads should ideally be above 80%.
[194] object · 8 fields
id
target-mapping-srr1552451-num_total
claim_id
claim-alignment
operation
null
expected_value
28322351
unit
reads in the library
tolerance
null
state
partial
note
Section 27: SRR1552451, num total 28322351. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[195] object · 8 fields
id
target-mapping-srr1552451-num_mapped
claim_id
claim-alignment
operation
null
expected_value
24794251
unit
reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552451, num mapped 24794251. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[196] object · 8 fields
id
target-mapping-srr1552451-prop
claim_id
claim-alignment
operation
null
expected_value
0.875
unit
proportion of reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552451, PropMapped 0.875. The paper states that the proportion of mapped reads should ideally be above 80%.
[197] object · 8 fields
id
target-mapping-srr1552452-num_total
claim_id
claim-alignment
operation
null
expected_value
31688348
unit
reads in the library
tolerance
null
state
partial
note
Section 27: SRR1552452, num total 31688348. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[198] object · 8 fields
id
target-mapping-srr1552452-num_mapped
claim_id
claim-alignment
operation
null
expected_value
27937620
unit
reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552452, num mapped 27937620. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[199] object · 8 fields
id
target-mapping-srr1552452-prop
claim_id
claim-alignment
operation
null
expected_value
0.882
unit
proportion of reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552452, PropMapped 0.882. The paper states that the proportion of mapped reads should ideally be above 80%.
[200] object · 8 fields
id
target-mapping-srr1552453-num_total
claim_id
claim-alignment
operation
null
expected_value
29614284
unit
reads in the library
tolerance
null
state
partial
note
Section 27: SRR1552453, num total 29614284. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[201] object · 8 fields
id
target-mapping-srr1552453-num_mapped
claim_id
claim-alignment
operation
null
expected_value
26074034
unit
reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552453, num mapped 26074034. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[202] object · 8 fields
id
target-mapping-srr1552453-prop
claim_id
claim-alignment
operation
null
expected_value
0.88
unit
proportion of reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552453, PropMapped 0.880. The paper states that the proportion of mapped reads should ideally be above 80%.
[203] object · 8 fields
id
target-mapping-srr1552454-num_total
claim_id
claim-alignment
operation
null
expected_value
27225012
unit
reads in the library
tolerance
null
state
partial
note
Section 27: SRR1552454, num total 27225012. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[204] object · 8 fields
id
target-mapping-srr1552454-num_mapped
claim_id
claim-alignment
operation
null
expected_value
24381742
unit
reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552454, num mapped 24381742. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[205] object · 8 fields
id
target-mapping-srr1552454-prop
claim_id
claim-alignment
operation
null
expected_value
0.896
unit
proportion of reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552454, PropMapped 0.896. The paper states that the proportion of mapped reads should ideally be above 80%.
[206] object · 8 fields
id
target-mapping-srr1552455-num_total
claim_id
claim-alignment
operation
null
expected_value
25433157
unit
reads in the library
tolerance
null
state
partial
note
Section 27: SRR1552455, num total 25433157. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[207] object · 8 fields
id
target-mapping-srr1552455-num_mapped
claim_id
claim-alignment
operation
null
expected_value
22813815
unit
reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552455, num mapped 22813815. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[208] object · 8 fields
id
target-mapping-srr1552455-prop
claim_id
claim-alignment
operation
null
expected_value
0.897
unit
proportion of reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552455, PropMapped 0.897. The paper states that the proportion of mapped reads should ideally be above 80%.
[209] object · 8 fields
id
target-mapping-srr1552444-num_total
claim_id
claim-alignment
operation
null
expected_value
27919481
unit
reads in the library
tolerance
null
state
partial
note
Section 27: SRR1552444, num total 27919481. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[210] object · 8 fields
id
target-mapping-srr1552444-num_mapped
claim_id
claim-alignment
operation
null
expected_value
23927833
unit
reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552444, num mapped 23927833. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[211] object · 8 fields
id
target-mapping-srr1552444-prop
claim_id
claim-alignment
operation
null
expected_value
0.857
unit
proportion of reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552444, PropMapped 0.857. The paper states that the proportion of mapped reads should ideally be above 80%.
[212] object · 8 fields
id
target-mapping-srr1552445-num_total
claim_id
claim-alignment
operation
null
expected_value
29731031
unit
reads in the library
tolerance
null
state
partial
note
Section 27: SRR1552445, num total 29731031. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[213] object · 8 fields
id
target-mapping-srr1552445-num_mapped
claim_id
claim-alignment
operation
null
expected_value
25487822
unit
reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552445, num mapped 25487822. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[214] object · 8 fields
id
target-mapping-srr1552445-prop
claim_id
claim-alignment
operation
null
expected_value
0.857
unit
proportion of reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552445, PropMapped 0.857. The paper states that the proportion of mapped reads should ideally be above 80%.
[215] object · 8 fields
id
target-mapping-srr1552446-num_total
claim_id
claim-alignment
operation
null
expected_value
29879070
unit
reads in the library
tolerance
null
state
partial
note
Section 27: SRR1552446, num total 29879070. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[216] object · 8 fields
id
target-mapping-srr1552446-num_mapped
claim_id
claim-alignment
operation
null
expected_value
25500318
unit
reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552446, num mapped 25500318. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[217] object · 8 fields
id
target-mapping-srr1552446-prop
claim_id
claim-alignment
operation
null
expected_value
0.853
unit
proportion of reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552446, PropMapped 0.853. The paper states that the proportion of mapped reads should ideally be above 80%.
[218] object · 8 fields
id
target-mapping-srr1552447-num_total
claim_id
claim-alignment
operation
null
expected_value
29245388
unit
reads in the library
tolerance
null
state
partial
note
Section 27: SRR1552447, num total 29245388. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[219] object · 8 fields
id
target-mapping-srr1552447-num_mapped
claim_id
claim-alignment
operation
null
expected_value
25187577
unit
reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552447, num mapped 25187577. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[220] object · 8 fields
id
target-mapping-srr1552447-prop
claim_id
claim-alignment
operation
null
expected_value
0.861
unit
proportion of reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552447, PropMapped 0.861. The paper states that the proportion of mapped reads should ideally be above 80%.
[221] object · 8 fields
id
target-mapping-srr1552448-num_total
claim_id
claim-alignment
operation
null
expected_value
31425424
unit
reads in the library
tolerance
null
state
partial
note
Section 27: SRR1552448, num total 31425424. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[222] object · 8 fields
id
target-mapping-srr1552448-num_mapped
claim_id
claim-alignment
operation
null
expected_value
27326500
unit
reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552448, num mapped 27326500. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[223] object · 8 fields
id
target-mapping-srr1552448-prop
claim_id
claim-alignment
operation
null
expected_value
0.87
unit
proportion of reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552448, PropMapped 0.870. The paper states that the proportion of mapped reads should ideally be above 80%.
[224] object · 8 fields
id
target-mapping-srr1552449-num_total
claim_id
claim-alignment
operation
null
expected_value
31276061
unit
reads in the library
tolerance
null
state
partial
note
Section 27: SRR1552449, num total 31276061. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[225] object · 8 fields
id
target-mapping-srr1552449-num_mapped
claim_id
claim-alignment
operation
null
expected_value
27204156
unit
reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552449, num mapped 27204156. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.
[226] object · 8 fields
id
target-mapping-srr1552449-prop
claim_id
claim-alignment
operation
null
expected_value
0.87
unit
proportion of reads mapped to a unique location
tolerance
null
state
partial
note
Section 27: SRR1552449, PropMapped 0.870. The paper states that the proportion of mapped reads should ideally be above 80%.
[227] object · 8 fields
id
target-kegg-mmu03008-n
claim_id
claim-pathway
operation
pathway_enrich
expected_value
75
unit
genes in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu03008 Ribosome biogenesis in eukaryot..., n 75. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[228] object · 8 fields
id
target-kegg-mmu03008-up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
1
unit
genes up in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu03008 Ribosome biogenesis in eukaryot..., up 1. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[229] object · 8 fields
id
target-kegg-mmu03008-down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
19
unit
genes down in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu03008 Ribosome biogenesis in eukaryot..., down 19. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[230] object · 8 fields
id
target-kegg-mmu03008-p_up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
0.404
unit
KEGG p-value, up-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu03008 Ribosome biogenesis in eukaryot..., p_up 4.04e-01. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[231] object · 8 fields
id
target-kegg-mmu03008-p_down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
3.23E-19
unit
KEGG p-value, down-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu03008 Ribosome biogenesis in eukaryot..., p_down 3.23e-19. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[232] object · 8 fields
id
target-kegg-mmu01100-n
claim_id
claim-pathway
operation
pathway_enrich
expected_value
1030
unit
genes in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu01100 Metabolic pathways, n 1030. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[233] object · 8 fields
id
target-kegg-mmu01100-up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
28
unit
genes up in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu01100 Metabolic pathways, up 28. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[234] object · 8 fields
id
target-kegg-mmu01100-down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
51
unit
genes down in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu01100 Metabolic pathways, down 51. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[235] object · 8 fields
id
target-kegg-mmu01100-p_up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
3.42E-10
unit
KEGG p-value, up-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu01100 Metabolic pathways, p_up 3.42e-10. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[236] object · 8 fields
id
target-kegg-mmu01100-p_down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
1.11E-15
unit
KEGG p-value, down-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu01100 Metabolic pathways, p_down 1.11e-15. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[237] object · 8 fields
id
target-kegg-mmu04110-n
claim_id
claim-pathway
operation
pathway_enrich
expected_value
120
unit
genes in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04110 Cell cycle, n 120. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[238] object · 8 fields
id
target-kegg-mmu04110-up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
1
unit
genes up in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04110 Cell cycle, up 1. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[239] object · 8 fields
id
target-kegg-mmu04110-down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
19
unit
genes down in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04110 Cell cycle, down 19. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[240] object · 8 fields
id
target-kegg-mmu04110-p_up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
0.563
unit
KEGG p-value, up-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04110 Cell cycle, p_up 5.63e-01. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[241] object · 8 fields
id
target-kegg-mmu04110-p_down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
3.78E-15
unit
KEGG p-value, down-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04110 Cell cycle, p_down 3.78e-15. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[242] object · 8 fields
id
target-kegg-mmu00230-n
claim_id
claim-pathway
operation
pathway_enrich
expected_value
152
unit
genes in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu00230 Purine metabolism, n 152. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[243] object · 8 fields
id
target-kegg-mmu00230-up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
2
unit
genes up in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu00230 Purine metabolism, up 2. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[244] object · 8 fields
id
target-kegg-mmu00230-down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
18
unit
genes down in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu00230 Purine metabolism, down 18. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[245] object · 8 fields
id
target-kegg-mmu00230-p_up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
0.28
unit
KEGG p-value, up-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu00230 Purine metabolism, p_up 2.80e-01. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[246] object · 8 fields
id
target-kegg-mmu00230-p_down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
3.45E-12
unit
KEGG p-value, down-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu00230 Purine metabolism, p_down 3.45e-12. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[247] object · 8 fields
id
target-kegg-mmu00240-n
claim_id
claim-pathway
operation
pathway_enrich
expected_value
96
unit
genes in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu00240 Pyrimidine metabolism, n 96. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[248] object · 8 fields
id
target-kegg-mmu00240-up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
0
unit
genes up in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu00240 Pyrimidine metabolism, up 0. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[249] object · 8 fields
id
target-kegg-mmu00240-down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
15
unit
genes down in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu00240 Pyrimidine metabolism, down 15. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[250] object · 8 fields
id
target-kegg-mmu00240-p_up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
1
unit
KEGG p-value, up-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu00240 Pyrimidine metabolism, p_up 1.00e+00. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[251] object · 8 fields
id
target-kegg-mmu00240-p_down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
3.86E-12
unit
KEGG p-value, down-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu00240 Pyrimidine metabolism, p_down 3.86e-12. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[252] object · 8 fields
id
target-kegg-mmu05150-n
claim_id
claim-pathway
operation
pathway_enrich
expected_value
30
unit
genes in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu05150 Staphylococcus aureus infection, n 30. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[253] object · 8 fields
id
target-kegg-mmu05150-up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
0
unit
genes up in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu05150 Staphylococcus aureus infection, up 0. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[254] object · 8 fields
id
target-kegg-mmu05150-down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
10
unit
genes down in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu05150 Staphylococcus aureus infection, down 10. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[255] object · 8 fields
id
target-kegg-mmu05150-p_up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
1
unit
KEGG p-value, up-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu05150 Staphylococcus aureus infection, p_up 1.00e+00. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[256] object · 8 fields
id
target-kegg-mmu05150-p_down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
4.78E-12
unit
KEGG p-value, down-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu05150 Staphylococcus aureus infection, p_down 4.78e-12. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[257] object · 8 fields
id
target-kegg-mmu04510-n
claim_id
claim-pathway
operation
pathway_enrich
expected_value
191
unit
genes in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04510 Focal adhesion, n 191. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[258] object · 8 fields
id
target-kegg-mmu04510-up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
13
unit
genes up in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04510 Focal adhesion, up 13. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[259] object · 8 fields
id
target-kegg-mmu04510-down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
9
unit
genes down in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04510 Focal adhesion, down 9. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[260] object · 8 fields
id
target-kegg-mmu04510-p_up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
7.22E-10
unit
KEGG p-value, up-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04510 Focal adhesion, p_up 7.22e-10. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[261] object · 8 fields
id
target-kegg-mmu04510-p_down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
0.00134
unit
KEGG p-value, down-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04510 Focal adhesion, p_down 1.34e-03. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[262] object · 8 fields
id
target-kegg-mmu04060-n
claim_id
claim-pathway
operation
pathway_enrich
expected_value
167
unit
genes in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04060 Cytokine-cytokine receptor inte..., n 167. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[263] object · 8 fields
id
target-kegg-mmu04060-up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
9
unit
genes up in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04060 Cytokine-cytokine receptor inte..., up 9. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[264] object · 8 fields
id
target-kegg-mmu04060-down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
16
unit
genes down in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04060 Cytokine-cytokine receptor inte..., down 16. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[265] object · 8 fields
id
target-kegg-mmu04060-p_up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
2.34E-6
unit
KEGG p-value, up-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04060 Cytokine-cytokine receptor inte..., p_up 2.34e-06. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[266] object · 8 fields
id
target-kegg-mmu04060-p_down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
1.35E-9
unit
KEGG p-value, down-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04060 Cytokine-cytokine receptor inte..., p_down 1.35e-09. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[267] object · 8 fields
id
target-kegg-mmu04514-n
claim_id
claim-pathway
operation
pathway_enrich
expected_value
112
unit
genes in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04514 Cell adhesion molecules (CAMs), n 112. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[268] object · 8 fields
id
target-kegg-mmu04514-up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
2
unit
genes up in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04514 Cell adhesion molecules (CAMs), up 2. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[269] object · 8 fields
id
target-kegg-mmu04514-down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
13
unit
genes down in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04514 Cell adhesion molecules (CAMs), down 13. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[270] object · 8 fields
id
target-kegg-mmu04514-p_up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
0.179
unit
KEGG p-value, up-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04514 Cell adhesion molecules (CAMs), p_up 1.79e-01. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[271] object · 8 fields
id
target-kegg-mmu04514-p_down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
4.72E-9
unit
KEGG p-value, down-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04514 Cell adhesion molecules (CAMs), p_down 4.72e-09. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[272] object · 8 fields
id
target-kegg-mmu04972-n
claim_id
claim-pathway
operation
pathway_enrich
expected_value
63
unit
genes in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04972 Pancreatic secretion, n 63. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[273] object · 8 fields
id
target-kegg-mmu04972-up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
8
unit
genes up in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04972 Pancreatic secretion, up 8. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[274] object · 8 fields
id
target-kegg-mmu04972-down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
4
unit
genes down in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04972 Pancreatic secretion, down 4. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[275] object · 8 fields
id
target-kegg-mmu04972-p_up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
1.14E-8
unit
KEGG p-value, up-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04972 Pancreatic secretion, p_up 1.14e-08. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[276] object · 8 fields
id
target-kegg-mmu04972-p_down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
0.011
unit
KEGG p-value, down-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04972 Pancreatic secretion, p_down 1.10e-02. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[277] object · 8 fields
id
target-kegg-mmu04970-n
claim_id
claim-pathway
operation
pathway_enrich
expected_value
63
unit
genes in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04970 Salivary secretion, n 63. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[278] object · 8 fields
id
target-kegg-mmu04970-up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
8
unit
genes up in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04970 Salivary secretion, up 8. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[279] object · 8 fields
id
target-kegg-mmu04970-down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
7
unit
genes down in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04970 Salivary secretion, down 7. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[280] object · 8 fields
id
target-kegg-mmu04970-p_up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
1.14E-8
unit
KEGG p-value, up-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04970 Salivary secretion, p_up 1.14e-08. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[281] object · 8 fields
id
target-kegg-mmu04970-p_down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
2.45E-5
unit
KEGG p-value, down-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04970 Salivary secretion, p_down 2.45e-05. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[282] object · 8 fields
id
target-kegg-mmu04610-n
claim_id
claim-pathway
operation
pathway_enrich
expected_value
47
unit
genes in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04610 Complement and coagulation casc..., n 47. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[283] object · 8 fields
id
target-kegg-mmu04610-up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
2
unit
genes up in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04610 Complement and coagulation casc..., up 2. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[284] object · 8 fields
id
target-kegg-mmu04610-down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
9
unit
genes down in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04610 Complement and coagulation casc..., down 9. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[285] object · 8 fields
id
target-kegg-mmu04610-p_up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
0.0414
unit
KEGG p-value, up-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04610 Complement and coagulation casc..., p_up 4.14e-02. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[286] object · 8 fields
id
target-kegg-mmu04610-p_down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
1.32E-8
unit
KEGG p-value, down-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04610 Complement and coagulation casc..., p_down 1.32e-08. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[287] object · 8 fields
id
target-kegg-mmu05166-n
claim_id
claim-pathway
operation
pathway_enrich
expected_value
245
unit
genes in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu05166 HTLV-I infection, n 245. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[288] object · 8 fields
id
target-kegg-mmu05166-up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
5
unit
genes up in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu05166 HTLV-I infection, up 5. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[289] object · 8 fields
id
target-kegg-mmu05166-down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
17
unit
genes down in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu05166 HTLV-I infection, down 17. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[290] object · 8 fields
id
target-kegg-mmu05166-p_up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
0.0271
unit
KEGG p-value, up-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu05166 HTLV-I infection, p_up 2.71e-02. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[291] object · 8 fields
id
target-kegg-mmu05166-p_down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
5.39E-8
unit
KEGG p-value, down-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu05166 HTLV-I infection, p_down 5.39e-08. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[292] object · 8 fields
id
target-kegg-mmu00100-n
claim_id
claim-pathway
operation
pathway_enrich
expected_value
18
unit
genes in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu00100 Steroid biosynthesis, n 18. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[293] object · 8 fields
id
target-kegg-mmu00100-up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
5
unit
genes up in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu00100 Steroid biosynthesis, up 5. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[294] object · 8 fields
id
target-kegg-mmu00100-down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
0
unit
genes down in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu00100 Steroid biosynthesis, down 0. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[295] object · 8 fields
id
target-kegg-mmu00100-p_up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
1.13E-7
unit
KEGG p-value, up-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu00100 Steroid biosynthesis, p_up 1.13e-07. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[296] object · 8 fields
id
target-kegg-mmu00100-p_down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
1
unit
KEGG p-value, down-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu00100 Steroid biosynthesis, p_down 1.00e+00. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[297] object · 8 fields
id
target-kegg-mmu04114-n
claim_id
claim-pathway
operation
pathway_enrich
expected_value
101
unit
genes in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04114 Oocyte meiosis, n 101. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[298] object · 8 fields
id
target-kegg-mmu04114-up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
2
unit
genes up in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04114 Oocyte meiosis, up 2. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[299] object · 8 fields
id
target-kegg-mmu04114-down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
11
unit
genes down in the pathway
tolerance
null
state
partial
note
Section 19: path:mmu04114 Oocyte meiosis, down 11. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[300] object · 8 fields
id
target-kegg-mmu04114-p_up
claim_id
claim-pathway
operation
pathway_enrich
expected_value
0.153
unit
KEGG p-value, up-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04114 Oocyte meiosis, p_up 1.53e-01. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
[301] object · 8 fields
id
target-kegg-mmu04114-p_down
claim_id
claim-pathway
operation
pathway_enrich
expected_value
1.43E-7
unit
KEGG p-value, down-regulated genes
tolerance
null
state
partial
note
Section 19: path:mmu04114 Oocyte meiosis, p_down 1.43e-07. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.
gaps array · 6 items
[0]
method.rna_seq_read_alignment
[1]
target.alignment_figures_not_comparable_across_runs
[2]
target.count_matrix_cells_not_published
[3]
target.fry_and_camera_results_not_published
[4]
target.gene_ontology_results_not_published
[5]
target.kegg_p_values_not_comparable_across_runs
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
availability_state
owned
tier_unlocked
R1
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
blocked
tier
R4
blocking_axis
method
blocked_on
method:rna_seq_read_alignment
axes object · 3 fields
method object · 5 fields
tier
R4
expressible
false
required_operations array · 4 items
[0]
normalise_counts
[1]
differential_expression_fit
[2]
fdr_bh
[3]
pathway_enrich
missing_operations array · 4 items
[0]
rna_seq_read_alignment
[1]
gene_count_quantification
[2]
normalise_counts_tmm
[3]
differential_expression_quasi_likelihood
basis
The DSL catalogue has no operation for: rna_seq_read_alignment, gene_count_quantification, normalise_counts_tmm, differential_expression_quasi_likelihood. The catalogue's normalise_counts is counts per million and its differential_expression_fit is a Welch t-test, so neither is edgeR's TMM normalisation nor its quasi-likelihood F-test.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The corpus capability table owns computational analysis.
data object · 6 fields
tier
R1
reachable
true
accessions array · 2 items
[0]
GSE60450
[1]
SRP045534
statements array · 1 item
[0]
Except for the targets file targets.txt, all data analyzed in the workflow is read automatically from public websites as part of the code. All software used is publicly available as part of Bioconductor 3.3, except for the fastq-dump utility, which can be downloaded from NCBI website as described in the text. The article includes the complete code necessary to reproduce the analyses shown.
basis
The GEO series resolves, its twelve samples are listed, and the twelve SRA runs resolve. No dataset was downloaded and no licence was read.
group_correspondence object · 6 fields
Basal virgin
B.virgin
Basal 18.5 dP
B.pregnant
Basal 2 dL
B.lactating
Luminal virgin
L.virgin
Luminal 18.5 dP
L.pregnant
Luminal 2 dL
L.lactating
can_run object · 3 fields
dsl_operations array · 4 items
[0]
normalise_counts
[1]
differential_expression_fit
[2]
fdr_bh
[3]
pathway_enrich
assets array · 2 items
[0]
source:pmid:27508061
[1]
data:geo:GSE60450
steps array · 0 items
must_build object · 5 fields
dsl_operations array · 4 items
[0] object · 3 fields
operation
rna_seq_read_alignment
unlocks_papers
null
priority
null
[1] object · 3 fields
operation
gene_count_quantification
unlocks_papers
null
priority
null
[2] object · 3 fields
operation
normalise_counts_tmm
unlocks_papers
null
priority
null
[3] object · 3 fields
operation
differential_expression_quasi_likelihood
unlocks_papers
null
priority
null
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE60450
gaps array · 1 item
[0]
method:rna_seq_read_alignment
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-11-03T19:28:53Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
8
usage object · 3 fields
prompt_tokens
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completion_tokens
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cached_tokens
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human_critique
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stages array · 1 item
[0] object · 4 fields
id
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reader
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minimax
gaps array · 3 items
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review.independent_reader
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review.machine_critique
[2]
review.human_critique
execution object · 5 fields
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status
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gaps array · 1 item
[0]
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provenance object · 7 fields
entities array · 3 items
[0] object · 3 fields
id
pmid:27508061
type
paper
label
pmid:27508061
[1] object · 3 fields
id
source:pmid:27508061
type
manuscript
label
PMID 27508061 full text
[2] object · 3 fields
id
data:geo:GSE60450
type
dataset
label
GEO GSE60450
activities array · 3 items
[0] object · 4 fields
id
activity-sci-assay-array-2026-11-03
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:27508061
type
paper
label
pmid:27508061
[1] object · 3 fields
id
source:pmid:27508061
type
manuscript
label
PMID 27508061 full text
[2] object · 3 fields
id
data:geo:GSE60450
type
dataset
label
GEO GSE60450
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-27508061
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extraction
used array · 1 item
[0]
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agent:minimax-reader
[2] object · 4 fields
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activity-resolve-GSE60450
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used array · 1 item
[0]
data:geo:GSE60450
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
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agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
id
agent:minimax-reader
type
software
label
MiniMax literature reader
source_run_id
sci-assay-array-2026-11-03
dsl_catalogue_fingerprint
f2132e96ae6c7a4e
capability_table_fingerprint
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snapshot_id
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lineage object · 4 fields
parent_id
pmid:27508061
parent_hash
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fork_of
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generation
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gaps array · 17 items
[0]
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[1]
asset:data:geo:GSE60450 not downloaded
[2]
asset:data:sra:SRP045534 licence not read
[3]
asset:data:sra:SRP045534 not downloaded
[4]
asset:reference:mm10 not downloaded
[5]
data.licence_not_stated_in_the_repository_record
[6]
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[7]
method.rna_seq_read_alignment
[8]
review.human_critique
[9]
review.independent_reader
[10]
review.machine_critique
[11]
step:run_analysis blocked on method:rna_seq_read_alignment
[12]
target.alignment_figures_not_comparable_across_runs
[13]
target.count_matrix_cells_not_published
[14]
target.fry_and_camera_results_not_published
[15]
target.gene_ontology_results_not_published
[16]
target.kegg_p_values_not_comparable_across_runs
assays array · 5 items
[0] object · 13 fields
role
data_generation
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rna-seq-read-alignment
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sha256:781215e3b5e462988c0f0a214b7462f32b5e18c58a59ff0e7366fdf7059c67a9
required_operations array · 1 item
[0]
rna_seq_read_alignment
support_state
unsupported
source_hashes object · 5 fields
assay_definition
sha256:096fe08e9f4c2a4cf0c344fce05384c3be6b532af00f0ebb651aeb690f0e1a45
assay_definition_digest
sha256:781215e3b5e462988c0f0a214b7462f32b5e18c58a59ff0e7366fdf7059c67a9
corpus_definition_alias
c3654ea6-862a-401b-8561-f5fd9b278ded
dsl_catalogue
f2132e96ae6c7a4e
source_text
3bf8a3f4c0135bde16e66f7f232937e6a89868783968461f69da3b9c8795dceb
confidence
1
evidence array · 2 items
[0]
Subread version 1.4.4 ( http://subread.sourceforge.net) was used to align the reads to the mouse mm10 genome and featureCounts was used to assign reads to Entrez Genes using RefSeq gene annotation.
[1]
The sequence reads can now be aligned to the mouse genome using the align function:
order_basis
paper_text_order:19240
depends_on array · 0 items
operations array · 0 items
id
assay:1
[1] object · 13 fields
role
data_generation
definition_id
rna-seq-gene-quantification
definition_version
0.1.0
definition_digest
sha256:a7731347e0ac054f8756d31ba6f586cb68a0e381b1946dfec53ef72bcddb1407
required_operations array · 1 item
[0]
gene_count_quantification
support_state
unsupported
source_hashes object · 5 fields
assay_definition
sha256:ffcc7cde4d8fadbff402bda8d9e8ca95a5fdf0788f18fbad297a2ad7569f381f
assay_definition_digest
sha256:a7731347e0ac054f8756d31ba6f586cb68a0e381b1946dfec53ef72bcddb1407
corpus_definition_alias
2d14b20d-4d4a-4f32-ae62-12eb89d2d2a2
dsl_catalogue
f2132e96ae6c7a4e
source_text
3bf8a3f4c0135bde16e66f7f232937e6a89868783968461f69da3b9c8795dceb
confidence
1
evidence array · 1 item
[0]
The read counts for each gene can be quantified using the featureCounts function in Rsubread.
order_basis
consumes_earlier_output
depends_on array · 1 item
[0]
assay:1
operations array · 0 items
id
assay:2
[2] object · 13 fields
role
normalisation
definition_id
rna-seq-count-filtering-and-normalisation
definition_version
0.1.0
definition_digest
sha256:029f48150fdbe3973df58cc1d9a63ea34bd5ba35c319469ee1cfd1249101c0fe
required_operations array · 2 items
[0]
normalise_counts
[1]
normalise_counts_tmm
support_state
partial
source_hashes object · 5 fields
assay_definition
sha256:e6870140eb683be699faca0423dc8601c085f696ba651a94bfe9bdee05489106
assay_definition_digest
sha256:029f48150fdbe3973df58cc1d9a63ea34bd5ba35c319469ee1cfd1249101c0fe
corpus_definition_alias
9acecdb9-4411-49af-9388-c808263d7e16
dsl_catalogue
f2132e96ae6c7a4e
source_text
3bf8a3f4c0135bde16e66f7f232937e6a89868783968461f69da3b9c8795dceb
confidence
1
evidence array · 2 items
[0]
For the current analysis, we keep genes that have CPM values above 0.5 in at least two libraries:
[1]
Normalization by trimmed mean of M values (TMM) 17 is performed by using the calcNormFactors function, which returns the DGEList argument with only the norm.factors changed.
order_basis
consumes_earlier_output
depends_on array · 1 item
[0]
assay:2
operations array · 1 item
[0] object · 5 fields
operation
normalise_counts
support_state
partial
input_contract object · 1 field
fields array · 6 items
[0]
counts_per_million
[1]
deterministic
[2]
library_sizes
[3]
log_counts
[4]
n_genes
[5]
n_samples
limitations array · 1 item
[0]
The catalogue's normalise_counts divides each count by its library size and returns counts per million and their log1p. It does not apply the paper's low-count filter, and it does not compute edgeR's TMM normalisation factors.
interpretation
A reproduction of this assay reproduces the paper's filter rule and its TMM factors. The catalogue's operation reproduces neither, so the two numbers this assay publishes are not the operation's output.
id
assay:3
[3] object · 13 fields
role
analysis
definition_id
rna-seq-differential-expression
definition_version
0.1.0
definition_digest
sha256:dfda866165c72d6cd1517a23e85867cdaa0adc1df88f9977b642792bdcdc7278
required_operations array · 3 items
[0]
differential_expression_fit
[1]
fdr_bh
[2]
differential_expression_quasi_likelihood
support_state
partial
source_hashes object · 5 fields
assay_definition
sha256:47bf2e85188384fddc7d6f5218de96a59230ad1577d39b8cb0c0e161275885b2
assay_definition_digest
sha256:dfda866165c72d6cd1517a23e85867cdaa0adc1df88f9977b642792bdcdc7278
corpus_definition_alias
bb104c14-fd8c-4c39-a3cd-be17740ca6f7
dsl_catalogue
f2132e96ae6c7a4e
source_text
3bf8a3f4c0135bde16e66f7f232937e6a89868783968461f69da3b9c8795dceb
confidence
1
evidence array · 3 items
[0]
The workflow uses edgeR’s quasi-likelihood pipeline (edgeR-quasi) for differential expression.
[1]
We will use QL F-tests instead of the more usual likelihood ratio tests (LRT) as they give stricter error rate control by accounting for the uncertainty in dispersion estimation:
[2]
In edgeR, this can be done using the glmTreat function.
order_basis
consumes_earlier_output
depends_on array · 1 item
[0]
assay:3
operations array · 2 items
[0] object · 5 fields
operation
differential_expression_fit
support_state
partial
input_contract object · 1 field
fields array · 5 items
[0]
deterministic
[1]
genes
[2]
n_control
[3]
n_genes
[4]
n_treatment
limitations array · 1 item
[0]
The catalogue's differential_expression_fit is a per-gene Welch t-test between two conditions. It is not edgeR's negative-binomial quasi-likelihood F-test, and it does not estimate dispersions.
interpretation
A reproduction of this assay answers the paper's contrast with the paper's dispersion estimates. The catalogue's operation does neither, so the logFCs and p-values this assay publishes are not the operation's output.
[1] object · 5 fields
operation
fdr_bh
support_state
partial
input_contract object · 1 field
fields array · 6 items
[0]
adjusted_p_values
[1]
deterministic
[2]
n
[3]
p_values
[4]
rejected
[5]
threshold
limitations array · 1 item
[0]
The catalogue's fdr_bh is the Benjamini-Hochberg adjustment, which is the adjustment the paper applies to its quasi-likelihood p-values.
interpretation
Given the paper's p-values, this operation reproduces the paper's FDR column.
id
assay:4
[4] object · 13 fields
role
analysis
definition_id
rna-seq-pathway-enrichment
definition_version
0.1.0
definition_digest
sha256:13560e312926f7eb0829d4fcf69d3ebb6bc2af081c63ea341def7d3ca69a1e27
required_operations array · 1 item
[0]
pathway_enrich
support_state
supported
source_hashes object · 5 fields
assay_definition
sha256:ec44213192bca3c385c095be319e89c59dee24f01df2d1f83546d8c7f97a51b1
assay_definition_digest
sha256:13560e312926f7eb0829d4fcf69d3ebb6bc2af081c63ea341def7d3ca69a1e27
corpus_definition_alias
58ae4ba5-8520-4fa3-a77c-d2193fa15634
dsl_catalogue
f2132e96ae6c7a4e
source_text
3bf8a3f4c0135bde16e66f7f232937e6a89868783968461f69da3b9c8795dceb
confidence
1
evidence array · 1 item
[0]
Another popular annotation database is the Kyoto Encyclopedia of Genes and Genomes (KEGG). Much smaller than GO, this is a curated database of molecular pathways and disease signatures. A KEGG analysis can be done exactly as for GO, but using the kegga function:
order_basis
consumes_earlier_output
depends_on array · 1 item
[0]
assay:4
operations array · 1 item
[0] object · 5 fields
operation
pathway_enrich
support_state
supported
input_contract object · 1 field
fields array · 4 items
[0]
background_size
[1]
deterministic
[2]
hit_size
[3]
pathways
limitations array · 1 item
[0]
The catalogue's pathway_enrich is a one-sided hypergeometric enrichment over a given pathway set. edgeR's kegga reports two p-values per pathway, one for the up-regulated genes and one for the down-regulated genes, and it reads the KEGG annotation from the Internet each time it runs.
interpretation
A reproduction of this assay names the pathway sets it used. The paper does not name the annotation it read, so the p-values it publishes cannot be compared numerically.
id
assay:5
Complete file 
{"sci_version": "1.5", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:27508061", "kind": "science-record", "revision": 4, "content_hash": "sha256:55ea50e300bb431a86d436951ca0ffa6f4e183dc3cde24b554526da6a21d4402", "created_at": "2026-11-03T19:42:08Z", "updated_at": "2026-11-04T13:34:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "sci-assay-array-2026-11-03"}, "paper": {"state": "complete", "title": "From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline", "doi": "10.12688/f1000research.8987.2", "pmid": "27508061", "authors": ["Yunshun Chen", "Aaron T. L. Lun", "Gordon K. Smyth"], "journal": "F1000Research", "year": 2016, "abstract": "In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most common aims of RNA-seq profiling is to identify genes or molecular pathways that are differentially expressed (DE) between two or more biological conditions. This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq data by providing a complete analysis of an RNA-seq experiment profiling epithelial cell subsets in the mouse mammary gland. The workflow uses R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, including alignment of read sequences, data exploration, differential expression analysis, visualization and pathway analysis. Read alignment and count quantification is conducted using the Rsubread package and the statistical analyses are performed using the edgeR package. The differential expression analysis uses the quasi-likelihood functionality of edgeR.", "claims": [{"id": "claim-ql-differential-expression", "statement": "Between basal lactating and basal pregnant mice, the edgeR quasi-likelihood F-test calls 5245 differentially expressed genes at a false discovery rate of 5%, and the top gene is Csn1s2b with a log2 fold change of 6.08.", "kind": "quantitative", "target": {"value": 5245.0, "unit": "genes called differentially expressed", "tolerance": null, "source": "In order to control the false discovery rate (FDR), multiple testing correction is performed using the Benjamini-Hochberg method. The top DE gene Csn1s2b has a large positive logFC, showing that it is far more highly expressed in the basal cells of lactating than pregnant mice. This gene is indeed known to be a major source of protein in milk."}, "evidence": [{"asset": "source:pmid:27508061", "locator": "sections[12] \"Testing for differential expression\" paragraph 8", "quote": "In order to control the false discovery rate (FDR), multiple testing correction is performed using the Benjamini-Hochberg method. The top DE gene Csn1s2b has a large positive logFC, showing that it is far more highly expressed in the basal cells of lactating than pregnant mice. This gene is indeed known to be a major source of protein in milk."}], "state": "complete"}, {"id": "claim-glmtreat-threshold", "statement": "Testing the same contrast against a fold-change threshold of 1.5 with glmTreat calls 1123 genes at a false discovery rate of 5%, and the paper states that about 1100 genes are detected.", "kind": "quantitative", "target": {"value": 1123.0, "unit": "genes called differentially expressed above the threshold", "tolerance": null, "source": "Note that the argument lfc is an abbreviation for “log-fold-change”. About 1100 genes are detected as DE with a FC significantly above 1.5 at an FDR cut-off of 5%."}, "evidence": [{"asset": "source:pmid:27508061", "locator": "sections[13] \"Differential expression relative to a fold-change threshold\" paragraph 5", "quote": "Note that the argument lfc is an abbreviation for “log-fold-change”. About 1100 genes are detected as DE with a FC significantly above 1.5 at an FDR cut-off of 5%."}], "state": "complete"}, {"id": "claim-interaction", "statement": "The interaction between mouse status and cell type — the change from pregnant to lactating in luminal cells less the same change in basal cells — is tested with the same quasi-likelihood F-test, and the top gene is Ppl with a log2 fold change of -4.62.", "kind": "quantitative", "target": {"value": -4.62, "unit": "log2 fold change (Ppl)", "tolerance": null, "source": "Suppose we are interested in testing whether the change in expression between lactating and pregnant mice is the same for basal cells as it is for luminal cells. In statistical terminology, this is the interaction effect between mouse status and cell type."}, "evidence": [{"asset": "source:pmid:27508061", "locator": "sections[16] \"Complicated contrasts\" paragraph 2", "quote": "Suppose we are interested in testing whether the change in expression between lactating and pregnant mice is the same for basal cells as it is for luminal cells. In statistical terminology, this is the interaction effect between mouse status and cell type."}], "state": "complete"}, {"id": "claim-counts", "statement": "The genewise count matrix the analysis starts from holds 27179 genes over twelve libraries, and the filter that keeps genes with counts per million above 0.5 in at least two libraries keeps 15653 of them.", "kind": "quantitative", "target": {"value": 15653.0, "unit": "genes kept by the filter", "tolerance": null, "source": "For the current analysis, we keep genes that have CPM values above 0.5 in at least two libraries:"}, "evidence": [{"asset": "source:pmid:27508061", "locator": "sections[6] \"Filtering to remove low counts\" paragraph 3", "quote": "For the current analysis, we keep genes that have CPM values above 0.5 in at least two libraries:"}], "state": "complete"}, {"id": "claim-normalisation", "statement": "The filtered libraries are normalised by the trimmed mean of M values, giving one factor per library, from 0.529 for MCL1.LE to 1.370 for MCL1.LA.", "kind": "quantitative", "target": {"value": 1.37, "unit": "TMM normalisation factor", "tolerance": null, "source": "Normalization by trimmed mean of M values (TMM) 17 is performed by using the calcNormFactors function, which returns the DGEList argument with only the norm.factors changed."}, "evidence": [{"asset": "source:pmid:27508061", "locator": "sections[7] \"Normalization for composition bias\" paragraph 2", "quote": "Normalization by trimmed mean of M values (TMM) 17 is performed by using the calcNormFactors function, which returns the DGEList argument with only the norm.factors changed."}], "state": "complete"}, {"id": "claim-alignment", "statement": "The reads are aligned to the GRCm38/mm10 mouse genome with subread 1.4.4, and between 85.3% and 89.7% of the reads are mapped to a unique location.", "kind": "quantitative", "target": {"value": 0.897, "unit": "proportion of reads mapped to a unique location", "tolerance": null, "source": "Subread version 1.4.4 ( http://subread.sourceforge.net) was used to align the reads to the mouse mm10 genome and featureCounts was used to assign reads to Entrez Genes using RefSeq gene annotation."}, "evidence": [{"asset": "source:pmid:27508061", "locator": "sections[2] \"Description of the biological experiment\" paragraph 3", "quote": "Subread version 1.4.4 ( http://subread.sourceforge.net) was used to align the reads to the mouse mm10 genome and featureCounts was used to assign reads to Entrez Genes using RefSeq gene annotation."}], "state": "complete"}, {"id": "claim-pathway", "statement": "The thresholded result is read for pathway enrichment with edgeR's kegga function, and the fifteen pathways the paper prints include the cell cycle pathway, which it reports as strongly down-regulated upon lactation.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27508061", "locator": "sections[19] \"KEGG pathway analysis\" paragraph 2", "quote": "Another popular annotation database is the Kyoto Encyclopedia of Genes and Genomes (KEGG). Much smaller than GO, this is a curated database of molecular pathways and disease signatures. A KEGG analysis can be done exactly as for GO, but using the kegga function:"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq data by providing a complete analysis of an RNA-seq experiment profiling epithelial cell subsets in the mouse mammary gland.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:27508061"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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The article includes the complete code necessary to reproduce the analyses shown.", "access_statement_kind": "availability_statement", "sample_accessions": ["GSM1480291", "GSM1480292", "GSM1480293", "GSM1480294", "GSM1480295", "GSM1480296", "GSM1480297", "GSM1480298", "GSM1480299", "GSM1480300", "GSM1480301", "GSM1480302"], "sample_count": 12, "group_sizes": {"Luminal virgin": 2, "Luminal 18.5 dP": 2, "Luminal 2 dL": 2, "Basal virgin": 2, "Basal 18.5 dP": 2, "Basal 2 dL": 2}, "group_sizes_basis": "The sample titles of the GEO series: Basal 18.5 dP (2), Basal 2 dL (2), Basal virgin (2), Luminal 18.5 dP (2), Luminal 2 dL (2), Luminal virgin (2).", "platform": "13112", "taxon": "Mus musculus", "title": "Transcriptome analysis of luminal and basal cell subpopulations in the lactating versus pregnant mammary gland", "resolution_checked_at": "2026-11-03T19:25:16Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:sra:SRP045534", "role": "raw", "format": "sra-study", "media_type": "application/x-sra", "uri": "https://www.ncbi.nlm.nih.gov/sra/?term=SRP045534", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "SRP045534", "version": null, "note": "The twelve raw FASTQ runs the paper aligns, one per library, and the study they belong to.", "structure": {"repository": "SRA", "study": "SRP045534", "bio_project": "PRJNA258286", "runs": [{"run": "SRR1552450", "sample": "GSM1480297", "cell_type": "B", "status": "virgin", "experiment": "SRX681991", "total_spots": 30109290, "total_bases": 3010929000, "title": "GSM1480297: Basal virgin #1; 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The publisher states no licence for the entry.", "structure": {"repository": "WEHI", "access_route": "the code entry URL", "fetched_at": "2026-11-03", "licence": "No licence stated by the publisher."}}, {"id": "code:wehi:edgeRQL.pdf", "role": "code", "format": "PDF", "media_type": "application/pdf", "uri": "http://bioinf.wehi.edu.au/edgeR/F1000Research2016/edgeRQL.pdf", "sha256": "sha256:76ea4da65b151b1bb78ba42b0d80c0e864632df0e13219fe968525a43efd2276", "bytes": 904232, "access": "open", "state": "verified", "reader": null, "reader_status": "available", "identifier": "edgeRQL.pdf", "version": null, "note": "The authors' own file, fetched and hashed on 3 November 2026. The publisher states no licence for the entry.", "structure": {"repository": "WEHI", "access_route": "the code entry URL", "fetched_at": "2026-11-03", "licence": "No licence stated by the publisher."}}, {"id": "reference:mm10", "role": "reference", "format": "fasta.gz", "media_type": "application/gzip", "uri": "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000001635.6_GRCm38.p4/GCA_000001635.6_GRCm38.p4_genomic.fna.gz", "sha256": null, "bytes": null, "access": "open", "state": "declared", "reader": null, "reader_status": "reader_required", "identifier": "GCA_000001635.6_GRCm38.p4", "version": "GRCm38 (Dec 2011)", "note": "The mouse genome build the paper indexes and aligns to, as the paper names it.", "structure": {"repository": "NCBI", "access_route": "the NCBI genome FTP path", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE60450 licence not read", "asset:data:geo:GSE60450 not downloaded", "asset:data:sra:SRP045534 licence not read", "asset:data:sra:SRP045534 not downloaded", "asset:reference:mm10 not downloaded", "data.licence_not_stated_in_the_repository_record"], "group_sizes": {"Basal 18.5 dP": 2, "Basal 2 dL": 2, "Basal virgin": 2, "Luminal 18.5 dP": 2, "Luminal 2 dL": 2, "Luminal virgin": 2}, "paper_group_sizes": {"sizes": {"B.lactating": 2, "B.pregnant": 2, "B.virgin": 2, "L.lactating": 2, "L.pregnant": 2, "L.virgin": 2}, "total": 12, "source": "There are therefore six groups of RNA samples, one for each combination of cell type and mouse status. Two biological replicates were collected for each group.", "reference_group": "B.pregnant"}}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "read_alignment", "specific": "Rsubread align to the GRCm38/mm10 reference", "label": "Read alignment", "dsl_operations": [], "missing_operations": ["rna_seq_read_alignment"], "expressible": false, "parameters": {"aligner": "Rsubread 1.4.4, align()", "reference": "GRCm38/mm10 (Dec 2011), GCA_000001635.6_GRCm38.p4", "index": "built with buildindex() from the genomic FASTA", "reads": "100 bp single-end FASTQ, about 30 million per sample", "mapped_reads": "only reads with a unique mapping location are reported"}, "data_shapes": ["FASTQ sequence reads"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Subread version 1.4.4 ( http://subread.sourceforge.net) was used to align the reads to the mouse mm10 genome and featureCounts was used to assign reads to Entrez Genes using RefSeq gene annotation."}}, {"id": "method-2", "family": "read_quantification", "specific": "Rsubread featureCounts against the inbuilt RefSeq annotation", "label": "Gene quantification", "dsl_operations": [], "missing_operations": ["gene_count_quantification"], "expressible": false, "parameters": {"tool": "Rsubread featureCounts", "annotation": "NCBI RefSeq, built in to Rsubread for mm10", "identifier": "Entrez Gene ID", "output": "a matrix of read counts per gene per sample"}, "data_shapes": ["BAM alignments", "gene annotation"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The read counts for each gene can be quantified using the featureCounts function in Rsubread."}}, {"id": "method-3", "family": "differential_expression", "specific": "low-count filtering by counts per million, then TMM normalisation", "label": "Count filtering and normalisation", "dsl_operations": ["normalise_counts"], "missing_operations": ["normalise_counts_tmm"], "expressible": false, "parameters": {"filter": "keep genes with CPM above 0.5 in at least 2 libraries", "keep.lib.sizes": false, "normalisation": "TMM, calcNormFactors()", "genes_kept": 15653, "genes_discarded": 10704}, "data_shapes": ["gene-level count matrix"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "For the current analysis, we keep genes that have CPM values above 0.5 in at least two libraries:"}}, {"id": "method-4", "family": "differential_expression", "specific": "edgeR quasi-likelihood F-test with Benjamini-Hochberg false discovery rate, and glmTreat against a fold-change threshold", "label": "Differential expression", "dsl_operations": ["differential_expression_fit", "fdr_bh"], "missing_operations": ["differential_expression_quasi_likelihood"], "expressible": false, "parameters": {"contrast": "B.lactating - B.pregnant", "test": "QL F-test, glmQLFTest()", "false_discovery_rate": "Benjamini-Hochberg, 5%", "threshold_test": "glmTreat(), lfc = log2(1.5) = 0.58", "design": "one-way layout, six groups, two biological replicates each"}, "data_shapes": ["normalised gene-level counts", "group labels"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We will use QL F-tests instead of the more usual likelihood ratio tests (LRT) as they give stricter error rate control by accounting for the uncertainty in dispersion estimation:"}}, {"id": "method-5", "family": "network_analysis", "specific": "KEGG pathway enrichment with edgeR's kegga on the thresholded result", "label": "Pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {"organism": "Mm", "pathways_printed": 15, "term_truncated_at": 34, "annotation": "KEGG, read from the Internet each time the analysis runs", "input": "the glmTreat result"}, "data_shapes": ["differential expression result", "pathway annotation"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "A KEGG analysis can be done exactly as for GO, but using the kegga function:"}}], "targets": [{"id": "target-ql-csn1s2b-logfc", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 6.08, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Csn1s2b, logFC; printed 6.08."}, {"id": "target-ql-csn1s2b-logcpm", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 10.19, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Csn1s2b, logCPM; printed 10.19."}, {"id": "target-ql-csn1s2b-f", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 421.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Csn1s2b, F; printed 421."}, {"id": "target-ql-csn1s2b-pvalue", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 4.78e-11, "unit": "p-value", "tolerance": 5e-14, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Csn1s2b, PValue; printed 4.78e-11."}, {"id": "target-ql-csn1s2b-fdr", "claim_id": "claim-ql-differential-expression", "operation": "fdr_bh", "expected_value": 7.48e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Csn1s2b, FDR; printed 7.48e-07."}, {"id": "target-ql-mrgprf-logfc", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 5.15, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Mrgprf, logFC; printed 5.15."}, {"id": "target-ql-mrgprf-logcpm", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 2.75, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Mrgprf, logCPM; printed 2.75."}, {"id": "target-ql-mrgprf-f", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 343.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Mrgprf, F; printed 343."}, {"id": "target-ql-mrgprf-pvalue", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 1.32e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Mrgprf, PValue; printed 1.32e-10."}, {"id": "target-ql-mrgprf-fdr", "claim_id": "claim-ql-differential-expression", "operation": "fdr_bh", "expected_value": 7.99e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Mrgprf, FDR; printed 7.99e-07."}, {"id": "target-ql-myof-logfc", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 2.32, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Myof, logFC; printed 2.32."}, {"id": "target-ql-myof-logcpm", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 6.45, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Myof, logCPM; printed 6.45."}, {"id": "target-ql-myof-f", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 322.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Myof, F; printed 322."}, {"id": "target-ql-myof-pvalue", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 1.97e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Myof, PValue; printed 1.97e-10."}, {"id": "target-ql-myof-fdr", "claim_id": "claim-ql-differential-expression", "operation": "fdr_bh", "expected_value": 7.99e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Myof, FDR; printed 7.99e-07."}, {"id": "target-ql-atp2b4-logfc", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 2.14, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Atp2b4, logFC; printed 2.14."}, {"id": "target-ql-atp2b4-logcpm", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 6.15, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Atp2b4, logCPM; printed 6.15."}, {"id": "target-ql-atp2b4-f", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 320.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Atp2b4, F; printed 320."}, {"id": "target-ql-atp2b4-pvalue", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 2.04e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Atp2b4, PValue; printed 2.04e-10."}, {"id": "target-ql-atp2b4-fdr", "claim_id": "claim-ql-differential-expression", "operation": "fdr_bh", "expected_value": 7.99e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Atp2b4, FDR; printed 7.99e-07."}, {"id": "target-ql-muc4-logfc", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": -7.17, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Muc4, logFC; printed -7.17."}, {"id": "target-ql-muc4-logcpm", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 6.06, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Muc4, logCPM; printed 6.06."}, {"id": "target-ql-muc4-f", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 308.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Muc4, F; printed 308."}, {"id": "target-ql-muc4-pvalue", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 2.6e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Muc4, PValue; printed 2.60e-10."}, {"id": "target-ql-muc4-fdr", "claim_id": "claim-ql-differential-expression", "operation": "fdr_bh", "expected_value": 8.15e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Muc4, FDR; printed 8.15e-07."}, {"id": "target-ql-micall2-logfc", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": -2.25, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Micall2, logFC; printed -2.25."}, {"id": "target-ql-micall2-logcpm", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 5.19, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Micall2, logCPM; printed 5.19."}, {"id": "target-ql-micall2-f", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 282.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Micall2, F; printed 282."}, {"id": "target-ql-micall2-pvalue", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 4.41e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Micall2, PValue; printed 4.41e-10."}, {"id": "target-ql-micall2-fdr", "claim_id": "claim-ql-differential-expression", "operation": "fdr_bh", "expected_value": 1.15e-06, "unit": "false discovery rate", "tolerance": 5e-09, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Micall2, FDR; printed 1.15e-06."}, {"id": "target-ql-wif1-logfc", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": -1.82, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Wif1, logFC; printed -1.82."}, {"id": "target-ql-wif1-logcpm", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 6.77, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Wif1, logCPM; printed 6.77."}, {"id": "target-ql-wif1-f", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 261.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Wif1, F; printed 261."}, {"id": "target-ql-wif1-pvalue", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 7.13e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Wif1, PValue; printed 7.13e-10."}, {"id": "target-ql-wif1-fdr", "claim_id": "claim-ql-differential-expression", "operation": "fdr_bh", "expected_value": 1.6e-06, "unit": "false discovery rate", "tolerance": 5e-09, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Wif1, FDR; printed 1.60e-06."}, {"id": "target-ql-cldn4-logfc", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": -5.32, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Cldn4, logFC; printed -5.32."}, {"id": "target-ql-cldn4-logcpm", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 9.87, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Cldn4, logCPM; printed 9.87."}, {"id": "target-ql-cldn4-f", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 298.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Cldn4, F; printed 298."}, {"id": "target-ql-cldn4-pvalue", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 9.12e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Cldn4, PValue; printed 9.12e-10."}, {"id": "target-ql-cldn4-fdr", "claim_id": "claim-ql-differential-expression", "operation": "fdr_bh", "expected_value": 1.74e-06, "unit": "false discovery rate", "tolerance": 5e-09, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Cldn4, FDR; printed 1.74e-06."}, {"id": "target-ql-tnni2-logfc", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 5.75, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Tnni2, logFC; printed 5.75."}, {"id": "target-ql-tnni2-logcpm", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 3.86, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Tnni2, logCPM; printed 3.86."}, {"id": "target-ql-tnni2-f", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 313.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Tnni2, F; printed 313."}, {"id": "target-ql-tnni2-pvalue", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 1e-09, "unit": "p-value", "tolerance": 5e-12, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Tnni2, PValue; printed 1.00e-09."}, {"id": "target-ql-tnni2-fdr", "claim_id": "claim-ql-differential-expression", "operation": "fdr_bh", "expected_value": 1.74e-06, "unit": "false discovery rate", "tolerance": 5e-09, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Tnni2, FDR; printed 1.74e-06."}, {"id": "target-ql-creb5-logfc", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 2.57, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Creb5, logFC; printed 2.57."}, {"id": "target-ql-creb5-logcpm", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 4.87, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Creb5, logCPM; printed 4.87."}, {"id": "target-ql-creb5-f", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 240.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Creb5, F; printed 240."}, {"id": "target-ql-creb5-pvalue", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 1.17e-09, "unit": "p-value", "tolerance": 5e-12, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Creb5, PValue; printed 1.17e-09."}, {"id": "target-ql-creb5-fdr", "claim_id": "claim-ql-differential-expression", "operation": "fdr_bh", "expected_value": 1.83e-06, "unit": "false discovery rate", "tolerance": 5e-09, "state": "complete", "note": "Section 12, the topTags printout of the quasi-likelihood F-test: Creb5, FDR; printed 1.83e-06."}, {"id": "target-glmtreat-csn1s2b-logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 6.08, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Csn1s2b, logFC; printed 6.08."}, {"id": "target-glmtreat-csn1s2b-unshrunk.logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 6.09, "unit": "log2 fold change, unshrunk (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Csn1s2b, unshrunk.logFC; printed 6.09."}, {"id": "target-glmtreat-csn1s2b-logcpm", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 10.19, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Csn1s2b, logCPM; printed 10.19."}, {"id": "target-glmtreat-csn1s2b-pvalue", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 5.94e-11, "unit": "p-value", "tolerance": 5e-14, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Csn1s2b, PValue; printed 5.94e-11."}, {"id": "target-glmtreat-csn1s2b-fdr", "claim_id": "claim-glmtreat-threshold", "operation": "fdr_bh", "expected_value": 9.3e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Csn1s2b, FDR; printed 9.30e-07."}, {"id": "target-glmtreat-mrgprf-logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 5.15, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Mrgprf, logFC; printed 5.15."}, {"id": "target-glmtreat-mrgprf-unshrunk.logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 5.15, "unit": "log2 fold change, unshrunk (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Mrgprf, unshrunk.logFC; printed 5.15."}, {"id": "target-glmtreat-mrgprf-logcpm", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 2.75, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Mrgprf, logCPM; printed 2.75."}, {"id": "target-glmtreat-mrgprf-pvalue", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 1.77e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Mrgprf, PValue; printed 1.77e-10."}, {"id": "target-glmtreat-mrgprf-fdr", "claim_id": "claim-glmtreat-threshold", "operation": "fdr_bh", "expected_value": 1.38e-06, "unit": "false discovery rate", "tolerance": 5e-09, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Mrgprf, FDR; printed 1.38e-06."}, {"id": "target-glmtreat-muc4-logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": -7.17, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Muc4, logFC; printed -7.17."}, {"id": "target-glmtreat-muc4-unshrunk.logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": -7.34, "unit": "log2 fold change, unshrunk (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Muc4, unshrunk.logFC; printed -7.34."}, {"id": "target-glmtreat-muc4-logcpm", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 6.06, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Muc4, logCPM; printed 6.06."}, {"id": "target-glmtreat-muc4-pvalue", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 3.98e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Muc4, PValue; printed 3.98e-10."}, {"id": "target-glmtreat-muc4-fdr", "claim_id": "claim-glmtreat-threshold", "operation": "fdr_bh", "expected_value": 2.07e-06, "unit": "false discovery rate", "tolerance": 5e-09, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Muc4, FDR; printed 2.07e-06."}, {"id": "target-glmtreat-myof-logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 2.32, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Myof, logFC; printed 2.32."}, {"id": "target-glmtreat-myof-unshrunk.logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 2.32, "unit": "log2 fold change, unshrunk (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Myof, unshrunk.logFC; printed 2.32."}, {"id": "target-glmtreat-myof-logcpm", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 6.45, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Myof, logCPM; printed 6.45."}, {"id": "target-glmtreat-myof-pvalue", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 7.82e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Myof, PValue; printed 7.82e-10."}, {"id": "target-glmtreat-myof-fdr", "claim_id": "claim-glmtreat-threshold", "operation": "fdr_bh", "expected_value": 2.69e-06, "unit": "false discovery rate", "tolerance": 5e-09, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Myof, FDR; printed 2.69e-06."}, {"id": "target-glmtreat-atp2b4-logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 2.14, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Atp2b4, logFC; printed 2.14."}, {"id": "target-glmtreat-atp2b4-unshrunk.logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 2.14, "unit": "log2 fold change, unshrunk (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Atp2b4, unshrunk.logFC; printed 2.14."}, {"id": "target-glmtreat-atp2b4-logcpm", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 6.15, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Atp2b4, logCPM; printed 6.15."}, {"id": "target-glmtreat-atp2b4-pvalue", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 1.01e-09, "unit": "p-value", "tolerance": 5e-12, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Atp2b4, PValue; printed 1.01e-09."}, {"id": "target-glmtreat-atp2b4-fdr", "claim_id": "claim-glmtreat-threshold", "operation": "fdr_bh", "expected_value": 2.69e-06, "unit": "false discovery rate", "tolerance": 5e-09, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Atp2b4, FDR; printed 2.69e-06."}, {"id": "target-glmtreat-cldn4-logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": -5.32, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Cldn4, logFC; printed -5.32."}, {"id": "target-glmtreat-cldn4-unshrunk.logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": -5.32, "unit": "log2 fold change, unshrunk (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Cldn4, unshrunk.logFC; printed -5.32."}, {"id": "target-glmtreat-cldn4-logcpm", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 9.87, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Cldn4, logCPM; printed 9.87."}, {"id": "target-glmtreat-cldn4-pvalue", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 1.14e-09, "unit": "p-value", "tolerance": 5e-12, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Cldn4, PValue; printed 1.14e-09."}, {"id": "target-glmtreat-cldn4-fdr", "claim_id": "claim-glmtreat-threshold", "operation": "fdr_bh", "expected_value": 2.69e-06, "unit": "false discovery rate", "tolerance": 5e-09, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Cldn4, FDR; printed 2.69e-06."}, {"id": "target-glmtreat-tnni2-logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 5.75, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Tnni2, logFC; printed 5.75."}, {"id": "target-glmtreat-tnni2-unshrunk.logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 5.76, "unit": "log2 fold change, unshrunk (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Tnni2, unshrunk.logFC; printed 5.76."}, {"id": "target-glmtreat-tnni2-logcpm", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 3.86, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Tnni2, logCPM; printed 3.86."}, {"id": "target-glmtreat-tnni2-pvalue", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 1.2e-09, "unit": "p-value", "tolerance": 5e-12, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Tnni2, PValue; printed 1.20e-09."}, {"id": "target-glmtreat-tnni2-fdr", "claim_id": "claim-glmtreat-threshold", "operation": "fdr_bh", "expected_value": 2.69e-06, "unit": "false discovery rate", "tolerance": 5e-09, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Tnni2, FDR; printed 2.69e-06."}, {"id": "target-glmtreat-micall2-logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": -2.25, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Micall2, logFC; printed -2.25."}, {"id": "target-glmtreat-micall2-unshrunk.logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": -2.25, "unit": "log2 fold change, unshrunk (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Micall2, unshrunk.logFC; printed -2.25."}, {"id": "target-glmtreat-micall2-logcpm", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 5.19, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Micall2, logCPM; printed 5.19."}, {"id": "target-glmtreat-micall2-pvalue", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 1.9e-09, "unit": "p-value", "tolerance": 5e-12, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Micall2, PValue; printed 1.90e-09."}, {"id": "target-glmtreat-micall2-fdr", "claim_id": "claim-glmtreat-threshold", "operation": "fdr_bh", "expected_value": 3.71e-06, "unit": "false discovery rate", "tolerance": 5e-09, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Micall2, FDR; printed 3.71e-06."}, {"id": "target-glmtreat-creb5-logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 2.57, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Creb5, logFC; printed 2.57."}, {"id": "target-glmtreat-creb5-unshrunk.logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 2.57, "unit": "log2 fold change, unshrunk (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Creb5, unshrunk.logFC; printed 2.57."}, {"id": "target-glmtreat-creb5-logcpm", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 4.87, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Creb5, logCPM; printed 4.87."}, {"id": "target-glmtreat-creb5-pvalue", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 3.55e-09, "unit": "p-value", "tolerance": 5e-12, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Creb5, PValue; printed 3.55e-09."}, {"id": "target-glmtreat-creb5-fdr", "claim_id": "claim-glmtreat-threshold", "operation": "fdr_bh", "expected_value": 6.18e-06, "unit": "false discovery rate", "tolerance": 5e-09, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Creb5, FDR; printed 6.18e-06."}, {"id": "target-glmtreat-igfbp6-logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 2.87, "unit": "log2 fold change (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Igfbp6, logFC; printed 2.87."}, {"id": "target-glmtreat-igfbp6-unshrunk.logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 2.87, "unit": "log2 fold change, unshrunk (basal lactating - basal pregnant)", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Igfbp6, unshrunk.logFC; printed 2.87."}, {"id": "target-glmtreat-igfbp6-logcpm", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 3.68, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Igfbp6, logCPM; printed 3.68."}, {"id": "target-glmtreat-igfbp6-pvalue", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 4.6e-09, "unit": "p-value", "tolerance": 5e-12, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Igfbp6, PValue; printed 4.60e-09."}, {"id": "target-glmtreat-igfbp6-fdr", "claim_id": "claim-glmtreat-threshold", "operation": "fdr_bh", "expected_value": 7.2e-06, "unit": "false discovery rate", "tolerance": 5e-09, "state": "complete", "note": "Section 13, the topTags printout of the glmTreat test: Igfbp6, FDR; printed 7.20e-06."}, {"id": "target-interaction-ppl-logfc", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": -4.62, "unit": "log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Ppl, logFC; printed -4.62."}, {"id": "target-interaction-ppl-logcpm", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 6.96, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Ppl, logCPM; printed 6.96."}, {"id": "target-interaction-ppl-f", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 524.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Ppl, F; printed 524."}, {"id": "target-interaction-ppl-pvalue", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 9.55e-12, "unit": "p-value", "tolerance": 5e-15, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Ppl, PValue; printed 9.55e-12."}, {"id": "target-interaction-ppl-fdr", "claim_id": "claim-interaction", "operation": "fdr_bh", "expected_value": 1.49e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Ppl, FDR; printed 1.49e-07."}, {"id": "target-interaction-creb5-logfc", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": -5.61, "unit": "log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Creb5, logFC; printed -5.61."}, {"id": "target-interaction-creb5-logcpm", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 4.87, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Creb5, logCPM; printed 4.87."}, {"id": "target-interaction-creb5-f", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 438.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Creb5, F; printed 438."}, {"id": "target-interaction-creb5-pvalue", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 2.91e-11, "unit": "p-value", "tolerance": 5e-14, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Creb5, PValue; printed 2.91e-11."}, {"id": "target-interaction-creb5-fdr", "claim_id": "claim-interaction", "operation": "fdr_bh", "expected_value": 2.13e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Creb5, FDR; printed 2.13e-07."}, {"id": "target-interaction-slc1a3-logfc", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 5.03, "unit": "log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Slc1a3, logFC; printed 5.03."}, {"id": "target-interaction-slc1a3-logcpm", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 3.65, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Slc1a3, logCPM; printed 3.65."}, {"id": "target-interaction-slc1a3-f", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 415.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Slc1a3, F; printed 415."}, {"id": "target-interaction-slc1a3-pvalue", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 4.09e-11, "unit": "p-value", "tolerance": 5e-14, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Slc1a3, PValue; printed 4.09e-11."}, {"id": "target-interaction-slc1a3-fdr", "claim_id": "claim-interaction", "operation": "fdr_bh", "expected_value": 2.13e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Slc1a3, FDR; printed 2.13e-07."}, {"id": "target-interaction-bc006965-logfc", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": -3.88, "unit": "log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: BC006965, logFC; printed -3.88."}, {"id": "target-interaction-bc006965-logcpm", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 4.68, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: BC006965, logCPM; printed 4.68."}, {"id": "target-interaction-bc006965-f", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 372.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: BC006965, F; printed 372."}, {"id": "target-interaction-bc006965-pvalue", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 8.11e-11, "unit": "p-value", "tolerance": 5e-14, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: BC006965, PValue; printed 8.11e-11."}, {"id": "target-interaction-bc006965-fdr", "claim_id": "claim-interaction", "operation": "fdr_bh", "expected_value": 2.86e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: BC006965, FDR; printed 2.86e-07."}, {"id": "target-interaction-ggt1-logfc", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 3.17, "unit": "log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Ggt1, logFC; printed 3.17."}, {"id": "target-interaction-ggt1-logcpm", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 6.38, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Ggt1, logCPM; printed 6.38."}, {"id": "target-interaction-ggt1-f", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 357.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Ggt1, F; printed 357."}, {"id": "target-interaction-ggt1-pvalue", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 1.04e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Ggt1, PValue; printed 1.04e-10."}, {"id": "target-interaction-ggt1-fdr", "claim_id": "claim-interaction", "operation": "fdr_bh", "expected_value": 2.86e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Ggt1, FDR; printed 2.86e-07."}, {"id": "target-interaction-slc25a1-logfc", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 3.47, "unit": "log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Slc25a1, logFC; printed 3.47."}, {"id": "target-interaction-slc25a1-logcpm", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 7.5, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Slc25a1, logCPM; printed 7.50."}, {"id": "target-interaction-slc25a1-f", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 354.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Slc25a1, F; printed 354."}, {"id": "target-interaction-slc25a1-pvalue", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 1.1e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Slc25a1, PValue; printed 1.10e-10."}, {"id": "target-interaction-slc25a1-fdr", "claim_id": "claim-interaction", "operation": "fdr_bh", "expected_value": 2.86e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Slc25a1, FDR; printed 2.86e-07."}, {"id": "target-interaction-sardh-logfc", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 2.92, "unit": "log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Sardh, logFC; printed 2.92."}, {"id": "target-interaction-sardh-logcpm", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 5.11, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Sardh, logCPM; printed 5.11."}, {"id": "target-interaction-sardh-f", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 342.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Sardh, F; printed 342."}, {"id": "target-interaction-sardh-pvalue", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 1.36e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Sardh, PValue; printed 1.36e-10."}, {"id": "target-interaction-sardh-fdr", "claim_id": "claim-interaction", "operation": "fdr_bh", "expected_value": 3.04e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Sardh, FDR; printed 3.04e-07."}, {"id": "target-interaction-rbp1-logfc", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": -4.4, "unit": "log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Rbp1, logFC; printed -4.40."}, {"id": "target-interaction-rbp1-logcpm", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 6.83, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Rbp1, logCPM; printed 6.83."}, {"id": "target-interaction-rbp1-f", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 337.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Rbp1, F; printed 337."}, {"id": "target-interaction-rbp1-pvalue", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 1.63e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Rbp1, PValue; printed 1.63e-10."}, {"id": "target-interaction-rbp1-fdr", "claim_id": "claim-interaction", "operation": "fdr_bh", "expected_value": 3.18e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Rbp1, FDR; printed 3.18e-07."}, {"id": "target-interaction-slc39a8-logfc", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 6.19, "unit": "log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Slc39a8, logFC; printed 6.19."}, {"id": "target-interaction-slc39a8-logcpm", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 5.07, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Slc39a8, logCPM; printed 5.07."}, {"id": "target-interaction-slc39a8-f", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 376.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Slc39a8, F; printed 376."}, {"id": "target-interaction-slc39a8-pvalue", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 1.83e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Slc39a8, PValue; printed 1.83e-10."}, {"id": "target-interaction-slc39a8-fdr", "claim_id": "claim-interaction", "operation": "fdr_bh", "expected_value": 3.18e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: Slc39a8, FDR; printed 3.18e-07."}, {"id": "target-interaction-f2rl1-logfc", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": -3.92, "unit": "log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: F2rl1, logFC; printed -3.92."}, {"id": "target-interaction-f2rl1-logcpm", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 5.61, "unit": "log2 counts per million", "tolerance": 0.005, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: F2rl1, logCPM; printed 5.61."}, {"id": "target-interaction-f2rl1-f", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 302.0, "unit": "F statistic", "tolerance": 0.0, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: F2rl1, F; printed 302."}, {"id": "target-interaction-f2rl1-pvalue", "claim_id": "claim-interaction", "operation": "differential_expression_fit", "expected_value": 2.93e-10, "unit": "p-value", "tolerance": 5e-13, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: F2rl1, PValue; printed 2.93e-10."}, {"id": "target-interaction-f2rl1-fdr", "claim_id": "claim-interaction", "operation": "fdr_bh", "expected_value": 4.2e-07, "unit": "false discovery rate", "tolerance": 5e-10, "state": "complete", "note": "Section 16, the topTags printout of the interaction contrast: F2rl1, FDR; printed 4.20e-07."}, {"id": "target-counts-genes", "claim_id": "claim-counts", "operation": "normalise_counts", "expected_value": 27179.0, "unit": "genes in the count matrix", "tolerance": 0.0, "state": "complete", "note": "Section 4: dim(GenewiseCounts) is 27179 genes by 13 columns, the gene length column and the twelve libraries."}, {"id": "target-counts-libraries", "claim_id": "claim-counts", "operation": "normalise_counts", "expected_value": 12.0, "unit": "libraries in the count matrix", "tolerance": 0.0, "state": "complete", "note": "Section 4: the count matrix carries one column per library, twelve of them, and one column of gene lengths."}, {"id": "target-filter-kept", "claim_id": "claim-counts", "operation": "normalise_counts", "expected_value": 15653.0, "unit": "genes kept by the filter", "tolerance": 0.0, "state": "complete", "note": "Section 6: the rule is CPM above 0.5 in at least two libraries, and it keeps 15653 genes."}, {"id": "target-filter-discarded", "claim_id": "claim-counts", "operation": "normalise_counts", "expected_value": 10704.0, "unit": "genes discarded by the filter", "tolerance": 0.0, "state": "complete", "note": "Section 6: the same rule discards 10704 genes."}, {"id": "target-ql-de-down", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 2757.0, "unit": "genes called down", "tolerance": 0.0, "state": "complete", "note": "Section 12: summary(decideTestsDGE) calls 2757 genes down."}, {"id": "target-ql-de-none", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 10408.0, "unit": "genes called none", "tolerance": 0.0, "state": "complete", "note": "Section 12: summary(decideTestsDGE) calls 10408 genes none."}, {"id": "target-ql-de-up", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 2488.0, "unit": "genes called up", "tolerance": 0.0, "state": "complete", "note": "Section 12: summary(decideTestsDGE) calls 2488 genes up."}, {"id": "target-glmtreat-de-down", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 723.0, "unit": "genes called down", "tolerance": 0.0, "state": "complete", "note": "Section 13: summary(decideTestsDGE) calls 723 genes down."}, {"id": "target-glmtreat-de-none", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 14530.0, "unit": "genes called none", "tolerance": 0.0, "state": "complete", "note": "Section 13: summary(decideTestsDGE) calls 14530 genes none."}, {"id": "target-glmtreat-de-up", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 400.0, "unit": "genes called up", "tolerance": 0.0, "state": "complete", "note": "Section 13: summary(decideTestsDGE) calls 400 genes up."}, {"id": "target-fdr-threshold", "claim_id": "claim-ql-differential-expression", "operation": "fdr_bh", "expected_value": 0.05, "unit": "exclusive false-discovery-rate threshold", "tolerance": 0.0, "state": "complete", "note": "Section 12: the false discovery rate is controlled at 5% by the Benjamini-Hochberg method."}, {"id": "target-ql-de-count-prose", "claim_id": "claim-ql-differential-expression", "operation": "differential_expression_fit", "expected_value": 5000.0, "unit": "genes (the paper states more than this)", "tolerance": null, "state": "partial", "note": "Section 12: the paper states there are in fact more than 5000 differentially expressed genes in this comparison. The count is a lower bound, not a value."}, {"id": "target-glmtreat-lfc-threshold", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 1.5, "unit": "fold-change threshold", "tolerance": 0.0, "state": "complete", "note": "Section 13: glmTreat is called with lfc = log2(1.5), so the test asks whether the fold changes are significantly greater than 1.5."}, {"id": "target-glmtreat-log2-threshold", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 0.58, "unit": "log2 fold-change threshold", "tolerance": 0.005, "state": "complete", "note": "Section 13: the paper states the threshold value of log 2(1.5) = 0.58."}, {"id": "target-glmtreat-de-count-prose", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 1100.0, "unit": "genes (the paper states about this many)", "tolerance": null, "state": "partial", "note": "Section 13: about 1100 genes are detected as differentially expressed with a fold change significantly above 1.5 at a false discovery rate of 5%. The count is approximate."}, {"id": "target-glmtreat-min-logfc", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 0.8, "unit": "log2 fold change, lower bound on the significant genes", "tolerance": null, "state": "partial", "note": "Section 13: all the statistically significant expression changes have logFC greater than 0.8. The value is a bound, not an estimate."}, {"id": "target-glmtreat-share-above-0.9", "claim_id": "claim-glmtreat-threshold", "operation": "differential_expression_fit", "expected_value": 97.0, "unit": "percent of the significant genes with logFC above 0.9", "tolerance": null, "state": "partial", "note": "Section 13: almost all (97%) of the significant genes have logFC greater than 0.9. The value is a share read off the paper's own summary."}, {"id": "target-libsize-mcl1.dg", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 23139638.0, "unit": "reads in the library after filtering", "tolerance": 0.0, "state": "complete", "note": "Section 7: MCL1.DG, group B.virgin, lib.size 23139638 after the filter and the TMM normalisation."}, {"id": "target-normfactor-mcl1.dg", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 1.235, "unit": "TMM normalisation factor", "tolerance": 0.0005, "state": "complete", "note": "Section 7: MCL1.DG, group B.virgin, norm.factors 1.235."}, {"id": "target-libsize-mcl1.dh", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 21689576.0, "unit": "reads in the library after filtering", "tolerance": 0.0, "state": "complete", "note": "Section 7: MCL1.DH, group B.virgin, lib.size 21689576 after the filter and the TMM normalisation."}, {"id": "target-normfactor-mcl1.dh", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 1.213, "unit": "TMM normalisation factor", "tolerance": 0.0005, "state": "complete", "note": "Section 7: MCL1.DH, group B.virgin, norm.factors 1.213."}, {"id": "target-libsize-mcl1.di", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 23976634.0, "unit": "reads in the library after filtering", "tolerance": 0.0, "state": "complete", "note": "Section 7: MCL1.DI, group B.pregnant, lib.size 23976634 after the filter and the TMM normalisation."}, {"id": "target-normfactor-mcl1.di", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 1.126, "unit": "TMM normalisation factor", "tolerance": 0.0005, "state": "complete", "note": "Section 7: MCL1.DI, group B.pregnant, norm.factors 1.126."}, {"id": "target-libsize-mcl1.dj", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 22546909.0, "unit": "reads in the library after filtering", "tolerance": 0.0, "state": "complete", "note": "Section 7: MCL1.DJ, group B.pregnant, lib.size 22546909 after the filter and the TMM normalisation."}, {"id": "target-normfactor-mcl1.dj", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 1.069, "unit": "TMM normalisation factor", "tolerance": 0.0005, "state": "complete", "note": "Section 7: MCL1.DJ, group B.pregnant, norm.factors 1.069."}, {"id": "target-libsize-mcl1.dk", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 21422164.0, "unit": "reads in the library after filtering", "tolerance": 0.0, "state": "complete", "note": "Section 7: MCL1.DK, group B.lactating, lib.size 21422164 after the filter and the TMM normalisation."}, {"id": "target-normfactor-mcl1.dk", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 1.036, "unit": "TMM normalisation factor", "tolerance": 0.0005, "state": "complete", "note": "Section 7: MCL1.DK, group B.lactating, norm.factors 1.036."}, {"id": "target-libsize-mcl1.dl", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 19918278.0, "unit": "reads in the library after filtering", "tolerance": 0.0, "state": "complete", "note": "Section 7: MCL1.DL, group B.lactating, lib.size 19918278 after the filter and the TMM normalisation."}, {"id": "target-normfactor-mcl1.dl", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 1.087, "unit": "TMM normalisation factor", "tolerance": 0.0005, "state": "complete", "note": "Section 7: MCL1.DL, group B.lactating, norm.factors 1.087."}, {"id": "target-libsize-mcl1.la", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 20276400.0, "unit": "reads in the library after filtering", "tolerance": 0.0, "state": "complete", "note": "Section 7: MCL1.LA, group L.virgin, lib.size 20276400 after the filter and the TMM normalisation."}, {"id": "target-normfactor-mcl1.la", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 1.37, "unit": "TMM normalisation factor", "tolerance": 0.0005, "state": "complete", "note": "Section 7: MCL1.LA, group L.virgin, norm.factors 1.370."}, {"id": "target-libsize-mcl1.lb", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 21571124.0, "unit": "reads in the library after filtering", "tolerance": 0.0, "state": "complete", "note": "Section 7: MCL1.LB, group L.virgin, lib.size 21571124 after the filter and the TMM normalisation."}, {"id": "target-normfactor-mcl1.lb", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 1.368, "unit": "TMM normalisation factor", "tolerance": 0.0005, "state": "complete", "note": "Section 7: MCL1.LB, group L.virgin, norm.factors 1.368."}, {"id": "target-libsize-mcl1.lc", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 22120647.0, "unit": "reads in the library after filtering", "tolerance": 0.0, "state": "complete", "note": "Section 7: MCL1.LC, group L.pregnant, lib.size 22120647 after the filter and the TMM normalisation."}, {"id": "target-normfactor-mcl1.lc", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 1.006, "unit": "TMM normalisation factor", "tolerance": 0.0005, "state": "complete", "note": "Section 7: MCL1.LC, group L.pregnant, norm.factors 1.006."}, {"id": "target-libsize-mcl1.ld", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 21879947.0, "unit": "reads in the library after filtering", "tolerance": 0.0, "state": "complete", "note": "Section 7: MCL1.LD, group L.pregnant, lib.size 21879947 after the filter and the TMM normalisation."}, {"id": "target-normfactor-mcl1.ld", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 0.924, "unit": "TMM normalisation factor", "tolerance": 0.0005, "state": "complete", "note": "Section 7: MCL1.LD, group L.pregnant, norm.factors 0.924."}, {"id": "target-libsize-mcl1.le", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 24660577.0, "unit": "reads in the library after filtering", "tolerance": 0.0, "state": "complete", "note": "Section 7: MCL1.LE, group L.lactating, lib.size 24660577 after the filter and the TMM normalisation."}, {"id": "target-normfactor-mcl1.le", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 0.529, "unit": "TMM normalisation factor", "tolerance": 0.0005, "state": "complete", "note": "Section 7: MCL1.LE, group L.lactating, norm.factors 0.529."}, {"id": "target-libsize-mcl1.lf", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 24602860.0, "unit": "reads in the library after filtering", "tolerance": 0.0, "state": "complete", "note": "Section 7: MCL1.LF, group L.lactating, lib.size 24602860 after the filter and the TMM normalisation."}, {"id": "target-normfactor-mcl1.lf", "claim_id": "claim-normalisation", "operation": "normalise_counts", "expected_value": 0.535, "unit": "TMM normalisation factor", "tolerance": 0.0005, "state": "complete", "note": "Section 7: MCL1.LF, group L.lactating, norm.factors 0.535."}, {"id": "target-mapping-srr1552450-num_total", "claim_id": "claim-alignment", "operation": null, "expected_value": 30109290.0, "unit": "reads in the library", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552450, num total 30109290. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552450-num_mapped", "claim_id": "claim-alignment", "operation": null, "expected_value": 26577308.0, "unit": "reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552450, num mapped 26577308. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552450-prop", "claim_id": "claim-alignment", "operation": null, "expected_value": 0.883, "unit": "proportion of reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552450, PropMapped 0.883. The paper states that the proportion of mapped reads should ideally be above 80%."}, {"id": "target-mapping-srr1552451-num_total", "claim_id": "claim-alignment", "operation": null, "expected_value": 28322351.0, "unit": "reads in the library", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552451, num total 28322351. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552451-num_mapped", "claim_id": "claim-alignment", "operation": null, "expected_value": 24794251.0, "unit": "reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552451, num mapped 24794251. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552451-prop", "claim_id": "claim-alignment", "operation": null, "expected_value": 0.875, "unit": "proportion of reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552451, PropMapped 0.875. The paper states that the proportion of mapped reads should ideally be above 80%."}, {"id": "target-mapping-srr1552452-num_total", "claim_id": "claim-alignment", "operation": null, "expected_value": 31688348.0, "unit": "reads in the library", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552452, num total 31688348. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552452-num_mapped", "claim_id": "claim-alignment", "operation": null, "expected_value": 27937620.0, "unit": "reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552452, num mapped 27937620. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552452-prop", "claim_id": "claim-alignment", "operation": null, "expected_value": 0.882, "unit": "proportion of reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552452, PropMapped 0.882. The paper states that the proportion of mapped reads should ideally be above 80%."}, {"id": "target-mapping-srr1552453-num_total", "claim_id": "claim-alignment", "operation": null, "expected_value": 29614284.0, "unit": "reads in the library", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552453, num total 29614284. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552453-num_mapped", "claim_id": "claim-alignment", "operation": null, "expected_value": 26074034.0, "unit": "reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552453, num mapped 26074034. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552453-prop", "claim_id": "claim-alignment", "operation": null, "expected_value": 0.88, "unit": "proportion of reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552453, PropMapped 0.880. The paper states that the proportion of mapped reads should ideally be above 80%."}, {"id": "target-mapping-srr1552454-num_total", "claim_id": "claim-alignment", "operation": null, "expected_value": 27225012.0, "unit": "reads in the library", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552454, num total 27225012. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552454-num_mapped", "claim_id": "claim-alignment", "operation": null, "expected_value": 24381742.0, "unit": "reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552454, num mapped 24381742. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552454-prop", "claim_id": "claim-alignment", "operation": null, "expected_value": 0.896, "unit": "proportion of reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552454, PropMapped 0.896. The paper states that the proportion of mapped reads should ideally be above 80%."}, {"id": "target-mapping-srr1552455-num_total", "claim_id": "claim-alignment", "operation": null, "expected_value": 25433157.0, "unit": "reads in the library", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552455, num total 25433157. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552455-num_mapped", "claim_id": "claim-alignment", "operation": null, "expected_value": 22813815.0, "unit": "reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552455, num mapped 22813815. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552455-prop", "claim_id": "claim-alignment", "operation": null, "expected_value": 0.897, "unit": "proportion of reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552455, PropMapped 0.897. The paper states that the proportion of mapped reads should ideally be above 80%."}, {"id": "target-mapping-srr1552444-num_total", "claim_id": "claim-alignment", "operation": null, "expected_value": 27919481.0, "unit": "reads in the library", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552444, num total 27919481. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552444-num_mapped", "claim_id": "claim-alignment", "operation": null, "expected_value": 23927833.0, "unit": "reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552444, num mapped 23927833. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552444-prop", "claim_id": "claim-alignment", "operation": null, "expected_value": 0.857, "unit": "proportion of reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552444, PropMapped 0.857. The paper states that the proportion of mapped reads should ideally be above 80%."}, {"id": "target-mapping-srr1552445-num_total", "claim_id": "claim-alignment", "operation": null, "expected_value": 29731031.0, "unit": "reads in the library", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552445, num total 29731031. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552445-num_mapped", "claim_id": "claim-alignment", "operation": null, "expected_value": 25487822.0, "unit": "reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552445, num mapped 25487822. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552445-prop", "claim_id": "claim-alignment", "operation": null, "expected_value": 0.857, "unit": "proportion of reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552445, PropMapped 0.857. The paper states that the proportion of mapped reads should ideally be above 80%."}, {"id": "target-mapping-srr1552446-num_total", "claim_id": "claim-alignment", "operation": null, "expected_value": 29879070.0, "unit": "reads in the library", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552446, num total 29879070. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552446-num_mapped", "claim_id": "claim-alignment", "operation": null, "expected_value": 25500318.0, "unit": "reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552446, num mapped 25500318. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552446-prop", "claim_id": "claim-alignment", "operation": null, "expected_value": 0.853, "unit": "proportion of reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552446, PropMapped 0.853. The paper states that the proportion of mapped reads should ideally be above 80%."}, {"id": "target-mapping-srr1552447-num_total", "claim_id": "claim-alignment", "operation": null, "expected_value": 29245388.0, "unit": "reads in the library", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552447, num total 29245388. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552447-num_mapped", "claim_id": "claim-alignment", "operation": null, "expected_value": 25187577.0, "unit": "reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552447, num mapped 25187577. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552447-prop", "claim_id": "claim-alignment", "operation": null, "expected_value": 0.861, "unit": "proportion of reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552447, PropMapped 0.861. The paper states that the proportion of mapped reads should ideally be above 80%."}, {"id": "target-mapping-srr1552448-num_total", "claim_id": "claim-alignment", "operation": null, "expected_value": 31425424.0, "unit": "reads in the library", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552448, num total 31425424. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552448-num_mapped", "claim_id": "claim-alignment", "operation": null, "expected_value": 27326500.0, "unit": "reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552448, num mapped 27326500. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552448-prop", "claim_id": "claim-alignment", "operation": null, "expected_value": 0.87, "unit": "proportion of reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552448, PropMapped 0.870. The paper states that the proportion of mapped reads should ideally be above 80%."}, {"id": "target-mapping-srr1552449-num_total", "claim_id": "claim-alignment", "operation": null, "expected_value": 31276061.0, "unit": "reads in the library", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552449, num total 31276061. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552449-num_mapped", "claim_id": "claim-alignment", "operation": null, "expected_value": 27204156.0, "unit": "reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552449, num mapped 27204156. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically."}, {"id": "target-mapping-srr1552449-prop", "claim_id": "claim-alignment", "operation": null, "expected_value": 0.87, "unit": "proportion of reads mapped to a unique location", "tolerance": null, "state": "partial", "note": "Section 27: SRR1552449, PropMapped 0.870. The paper states that the proportion of mapped reads should ideally be above 80%."}, {"id": "target-kegg-mmu03008-n", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 75.0, "unit": "genes in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu03008 Ribosome biogenesis in eukaryot..., n 75. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu03008-up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 1.0, "unit": "genes up in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu03008 Ribosome biogenesis in eukaryot..., up 1. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu03008-down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 19.0, "unit": "genes down in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu03008 Ribosome biogenesis in eukaryot..., down 19. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu03008-p_up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 0.404, "unit": "KEGG p-value, up-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu03008 Ribosome biogenesis in eukaryot..., p_up 4.04e-01. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu03008-p_down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 3.23e-19, "unit": "KEGG p-value, down-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu03008 Ribosome biogenesis in eukaryot..., p_down 3.23e-19. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu01100-n", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 1030.0, "unit": "genes in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu01100 Metabolic pathways, n 1030. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu01100-up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 28.0, "unit": "genes up in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu01100 Metabolic pathways, up 28. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu01100-down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 51.0, "unit": "genes down in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu01100 Metabolic pathways, down 51. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu01100-p_up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 3.42e-10, "unit": "KEGG p-value, up-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu01100 Metabolic pathways, p_up 3.42e-10. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu01100-p_down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 1.11e-15, "unit": "KEGG p-value, down-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu01100 Metabolic pathways, p_down 1.11e-15. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04110-n", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 120.0, "unit": "genes in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04110 Cell cycle, n 120. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04110-up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 1.0, "unit": "genes up in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04110 Cell cycle, up 1. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04110-down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 19.0, "unit": "genes down in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04110 Cell cycle, down 19. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04110-p_up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 0.563, "unit": "KEGG p-value, up-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04110 Cell cycle, p_up 5.63e-01. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04110-p_down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 3.78e-15, "unit": "KEGG p-value, down-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04110 Cell cycle, p_down 3.78e-15. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu00230-n", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 152.0, "unit": "genes in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu00230 Purine metabolism, n 152. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu00230-up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 2.0, "unit": "genes up in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu00230 Purine metabolism, up 2. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu00230-down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 18.0, "unit": "genes down in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu00230 Purine metabolism, down 18. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu00230-p_up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 0.28, "unit": "KEGG p-value, up-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu00230 Purine metabolism, p_up 2.80e-01. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu00230-p_down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 3.45e-12, "unit": "KEGG p-value, down-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu00230 Purine metabolism, p_down 3.45e-12. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu00240-n", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 96.0, "unit": "genes in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu00240 Pyrimidine metabolism, n 96. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu00240-up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 0.0, "unit": "genes up in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu00240 Pyrimidine metabolism, up 0. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu00240-down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 15.0, "unit": "genes down in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu00240 Pyrimidine metabolism, down 15. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu00240-p_up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 1.0, "unit": "KEGG p-value, up-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu00240 Pyrimidine metabolism, p_up 1.00e+00. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu00240-p_down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 3.86e-12, "unit": "KEGG p-value, down-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu00240 Pyrimidine metabolism, p_down 3.86e-12. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu05150-n", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 30.0, "unit": "genes in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu05150 Staphylococcus aureus infection, n 30. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu05150-up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 0.0, "unit": "genes up in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu05150 Staphylococcus aureus infection, up 0. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu05150-down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 10.0, "unit": "genes down in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu05150 Staphylococcus aureus infection, down 10. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu05150-p_up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 1.0, "unit": "KEGG p-value, up-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu05150 Staphylococcus aureus infection, p_up 1.00e+00. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu05150-p_down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 4.78e-12, "unit": "KEGG p-value, down-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu05150 Staphylococcus aureus infection, p_down 4.78e-12. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04510-n", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 191.0, "unit": "genes in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04510 Focal adhesion, n 191. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04510-up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 13.0, "unit": "genes up in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04510 Focal adhesion, up 13. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04510-down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 9.0, "unit": "genes down in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04510 Focal adhesion, down 9. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04510-p_up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 7.22e-10, "unit": "KEGG p-value, up-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04510 Focal adhesion, p_up 7.22e-10. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04510-p_down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 0.00134, "unit": "KEGG p-value, down-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04510 Focal adhesion, p_down 1.34e-03. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04060-n", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 167.0, "unit": "genes in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04060 Cytokine-cytokine receptor inte..., n 167. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04060-up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 9.0, "unit": "genes up in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04060 Cytokine-cytokine receptor inte..., up 9. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04060-down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 16.0, "unit": "genes down in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04060 Cytokine-cytokine receptor inte..., down 16. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04060-p_up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 2.34e-06, "unit": "KEGG p-value, up-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04060 Cytokine-cytokine receptor inte..., p_up 2.34e-06. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04060-p_down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 1.35e-09, "unit": "KEGG p-value, down-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04060 Cytokine-cytokine receptor inte..., p_down 1.35e-09. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04514-n", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 112.0, "unit": "genes in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04514 Cell adhesion molecules (CAMs), n 112. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04514-up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 2.0, "unit": "genes up in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04514 Cell adhesion molecules (CAMs), up 2. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04514-down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 13.0, "unit": "genes down in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04514 Cell adhesion molecules (CAMs), down 13. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04514-p_up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 0.179, "unit": "KEGG p-value, up-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04514 Cell adhesion molecules (CAMs), p_up 1.79e-01. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04514-p_down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 4.72e-09, "unit": "KEGG p-value, down-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04514 Cell adhesion molecules (CAMs), p_down 4.72e-09. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04972-n", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 63.0, "unit": "genes in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04972 Pancreatic secretion, n 63. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04972-up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 8.0, "unit": "genes up in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04972 Pancreatic secretion, up 8. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04972-down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 4.0, "unit": "genes down in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04972 Pancreatic secretion, down 4. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04972-p_up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 1.14e-08, "unit": "KEGG p-value, up-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04972 Pancreatic secretion, p_up 1.14e-08. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04972-p_down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 0.011, "unit": "KEGG p-value, down-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04972 Pancreatic secretion, p_down 1.10e-02. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04970-n", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 63.0, "unit": "genes in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04970 Salivary secretion, n 63. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04970-up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 8.0, "unit": "genes up in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04970 Salivary secretion, up 8. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04970-down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 7.0, "unit": "genes down in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04970 Salivary secretion, down 7. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04970-p_up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 1.14e-08, "unit": "KEGG p-value, up-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04970 Salivary secretion, p_up 1.14e-08. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04970-p_down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 2.45e-05, "unit": "KEGG p-value, down-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04970 Salivary secretion, p_down 2.45e-05. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04610-n", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 47.0, "unit": "genes in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04610 Complement and coagulation casc..., n 47. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04610-up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 2.0, "unit": "genes up in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04610 Complement and coagulation casc..., up 2. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04610-down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 9.0, "unit": "genes down in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04610 Complement and coagulation casc..., down 9. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04610-p_up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 0.0414, "unit": "KEGG p-value, up-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04610 Complement and coagulation casc..., p_up 4.14e-02. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04610-p_down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 1.32e-08, "unit": "KEGG p-value, down-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04610 Complement and coagulation casc..., p_down 1.32e-08. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu05166-n", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 245.0, "unit": "genes in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu05166 HTLV-I infection, n 245. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu05166-up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 5.0, "unit": "genes up in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu05166 HTLV-I infection, up 5. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu05166-down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 17.0, "unit": "genes down in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu05166 HTLV-I infection, down 17. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu05166-p_up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 0.0271, "unit": "KEGG p-value, up-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu05166 HTLV-I infection, p_up 2.71e-02. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu05166-p_down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 5.39e-08, "unit": "KEGG p-value, down-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu05166 HTLV-I infection, p_down 5.39e-08. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu00100-n", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 18.0, "unit": "genes in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu00100 Steroid biosynthesis, n 18. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu00100-up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 5.0, "unit": "genes up in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu00100 Steroid biosynthesis, up 5. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu00100-down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 0.0, "unit": "genes down in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu00100 Steroid biosynthesis, down 0. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu00100-p_up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 1.13e-07, "unit": "KEGG p-value, up-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu00100 Steroid biosynthesis, p_up 1.13e-07. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu00100-p_down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 1.0, "unit": "KEGG p-value, down-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu00100 Steroid biosynthesis, p_down 1.00e+00. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04114-n", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 101.0, "unit": "genes in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04114 Oocyte meiosis, n 101. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04114-up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 2.0, "unit": "genes up in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04114 Oocyte meiosis, up 2. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04114-down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 11.0, "unit": "genes down in the pathway", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04114 Oocyte meiosis, down 11. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04114-p_up", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 0.153, "unit": "KEGG p-value, up-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04114 Oocyte meiosis, p_up 1.53e-01. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}, {"id": "target-kegg-mmu04114-p_down", "claim_id": "claim-pathway", "operation": "pathway_enrich", "expected_value": 1.43e-07, "unit": "KEGG p-value, down-regulated genes", "tolerance": null, "state": "partial", "note": "Section 19: path:mmu04114 Oocyte meiosis, p_down 1.43e-07. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs."}], "gaps": ["method.rna_seq_read_alignment", "target.alignment_figures_not_comparable_across_runs", "target.count_matrix_cells_not_published", "target.fry_and_camera_results_not_published", "target.gene_ontology_results_not_published", "target.kegg_p_values_not_comparable_across_runs"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:rna_seq_read_alignment", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh", "pathway_enrich"], "missing_operations": ["rna_seq_read_alignment", "gene_count_quantification", "normalise_counts_tmm", "differential_expression_quasi_likelihood"], "basis": "The DSL catalogue has no operation for: rna_seq_read_alignment, gene_count_quantification, normalise_counts_tmm, differential_expression_quasi_likelihood. The catalogue's normalise_counts is counts per million and its differential_expression_fit is a Welch t-test, so neither is edgeR's TMM normalisation nor its quasi-likelihood F-test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The corpus capability table owns computational analysis."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE60450", "SRP045534"], "statements": ["Except for the targets file targets.txt, all data analyzed in the workflow is read automatically from public websites as part of the code. All software used is publicly available as part of Bioconductor 3.3, except for the fastq-dump utility, which can be downloaded from NCBI website as described in the text. The article includes the complete code necessary to reproduce the analyses shown."], "basis": "The GEO series resolves, its twelve samples are listed, and the twelve SRA runs resolve. No dataset was downloaded and no licence was read.", "group_correspondence": {"Basal virgin": "B.virgin", "Basal 18.5 dP": "B.pregnant", "Basal 2 dL": "B.lactating", "Luminal virgin": "L.virgin", "Luminal 18.5 dP": "L.pregnant", "Luminal 2 dL": "L.lactating"}}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh", "pathway_enrich"], "assets": ["source:pmid:27508061", "data:geo:GSE60450"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "rna_seq_read_alignment", "unlocks_papers": null, "priority": null}, {"operation": "gene_count_quantification", "unlocks_papers": null, "priority": null}, {"operation": "normalise_counts_tmm", "unlocks_papers": null, "priority": null}, {"operation": "differential_expression_quasi_likelihood", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE60450"]}, "gaps": ["method:rna_seq_read_alignment"]}, "review": {"state": "partial", 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{"parent_id": "pmid:27508061", "parent_hash": "sha256:f636045823884644379c50441f91cae48ae74b4b59cd302e940a770a09d4440e", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE60450 licence not read", "asset:data:geo:GSE60450 not downloaded", "asset:data:sra:SRP045534 licence not read", "asset:data:sra:SRP045534 not downloaded", "asset:reference:mm10 not downloaded", "data.licence_not_stated_in_the_repository_record", "execution.not_run", "method.rna_seq_read_alignment", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:rna_seq_read_alignment", "target.alignment_figures_not_comparable_across_runs", "target.count_matrix_cells_not_published", "target.fry_and_camera_results_not_published", "target.gene_ontology_results_not_published", "target.kegg_p_values_not_comparable_across_runs"], "assays": [{"role": "data_generation", "definition_id": "rna-seq-read-alignment", "definition_version": "0.1.0", 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{"role": "data_generation", "definition_id": "rna-seq-gene-quantification", "definition_version": "0.1.0", "definition_digest": "sha256:a7731347e0ac054f8756d31ba6f586cb68a0e381b1946dfec53ef72bcddb1407", "required_operations": ["gene_count_quantification"], "support_state": "unsupported", "source_hashes": {"assay_definition": "sha256:ffcc7cde4d8fadbff402bda8d9e8ca95a5fdf0788f18fbad297a2ad7569f381f", "assay_definition_digest": "sha256:a7731347e0ac054f8756d31ba6f586cb68a0e381b1946dfec53ef72bcddb1407", "corpus_definition_alias": "2d14b20d-4d4a-4f32-ae62-12eb89d2d2a2", "dsl_catalogue": "f2132e96ae6c7a4e", "source_text": "3bf8a3f4c0135bde16e66f7f232937e6a89868783968461f69da3b9c8795dceb"}, "confidence": 1.0, "evidence": ["The read counts for each gene can be quantified using the featureCounts function in Rsubread."], "order_basis": "consumes_earlier_output", "depends_on": ["assay:1"], "operations": [], "id": "assay:2"}, {"role": "normalisation", "definition_id": 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The catalogue's operation does neither, so the logFCs and p-values this assay publishes are not the operation's output."}, {"operation": "fdr_bh", "support_state": "partial", "input_contract": {"fields": ["adjusted_p_values", "deterministic", "n", "p_values", "rejected", "threshold"]}, "limitations": ["The catalogue's fdr_bh is the Benjamini-Hochberg adjustment, which is the adjustment the paper applies to its quasi-likelihood p-values."], "interpretation": "Given the paper's p-values, this operation reproduces the paper's FDR column."}], "id": "assay:4"}, {"role": "analysis", "definition_id": "rna-seq-pathway-enrichment", "definition_version": "0.1.0", "definition_digest": "sha256:13560e312926f7eb0829d4fcf69d3ebb6bc2af081c63ea341def7d3ca69a1e27", "required_operations": ["pathway_enrich"], "support_state": "supported", "source_hashes": {"assay_definition": "sha256:ec44213192bca3c385c095be319e89c59dee24f01df2d1f83546d8c7f97a51b1", "assay_definition_digest": "sha256:13560e312926f7eb0829d4fcf69d3ebb6bc2af081c63ea341def7d3ca69a1e27", "corpus_definition_alias": "58ae4ba5-8520-4fa3-a77c-d2193fa15634", "dsl_catalogue": "f2132e96ae6c7a4e", "source_text": "3bf8a3f4c0135bde16e66f7f232937e6a89868783968461f69da3b9c8795dceb"}, "confidence": 1.0, "evidence": ["Another popular annotation database is the Kyoto Encyclopedia of Genes and Genomes (KEGG). 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