{"data":{"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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE60450"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:rna_seq_read_alignment", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {"contrast": "B.lactating - B.pregnant", "reference_group": "B.pregnant", "false_discovery_rate": "Benjamini-Hochberg, 5%", "threshold_test": "glmTreat(), lfc = log2(1.5) = 0.58"}, "inputs": ["data:geo:GSE60450"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:rna_seq_read_alignment"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:27508061", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12688/f1000research.8987.2", "sha256": "sha256:3bf8a3f4c0135bde16e66f7f232937e6a89868783968461f69da3b9c8795dceb", "bytes": 60617, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12688/f1000research.8987.2", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4934518", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE60450", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60450", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE60450", "version": null, "note": "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.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "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.", "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; Mus musculus; RNA-Seq", "resolves": true}, {"run": "SRR1552451", "sample": "GSM1480298", "cell_type": "B", "status": "virgin", "experiment": "SRX681992", "total_spots": 28322351, "total_bases": 2832235100, "title": "GSM1480298: Basal virgin #2; Mus musculus; RNA-Seq", "resolves": true}, {"run": "SRR1552452", "sample": "GSM1480299", "cell_type": "B", "status": "pregnant", "experiment": "SRX681993", "total_spots": 31688348, "total_bases": 3168834800, "title": "GSM1480299: Basal 18.5 dP #1; Mus musculus; RNA-Seq", "resolves": true}, {"run": "SRR1552453", "sample": "GSM1480300", "cell_type": "B", "status": "pregnant", "experiment": "SRX681994", "total_spots": 29614284, "total_bases": 2961428400, "title": "GSM1480300: Basal 18.5 dP #2; Mus musculus; RNA-Seq", "resolves": true}, {"run": "SRR1552454", "sample": "GSM1480301", "cell_type": "B", "status": "lactating", "experiment": "SRX681995", "total_spots": 27225012, "total_bases": 2722501200, "title": "GSM1480301: Basal 2 dL #1; Mus musculus; RNA-Seq", "resolves": true}, {"run": "SRR1552455", "sample": "GSM1480302", "cell_type": "B", "status": "lactating", "experiment": "SRX681996", "total_spots": 25433157, "total_bases": 2543315700, "title": "GSM1480302: Basal 2 dL #2; Mus musculus; RNA-Seq", "resolves": true}, {"run": "SRR1552444", "sample": "GSM1480291", "cell_type": "L", "status": "virgin", "experiment": "SRX681985", "total_spots": 27919481, "total_bases": 2791948100, "title": "GSM1480291: Luminal virgin #1; Mus musculus; RNA-Seq", "resolves": true}, {"run": "SRR1552445", "sample": "GSM1480292", "cell_type": "L", "status": "virgin", "experiment": "SRX681986", "total_spots": 29731031, "total_bases": 2973103100, "title": "GSM1480292: Luminal virgin #2; Mus musculus; RNA-Seq", "resolves": true}, {"run": "SRR1552446", "sample": "GSM1480293", "cell_type": "L", "status": "pregnant", "experiment": "SRX681987", "total_spots": 29879070, "total_bases": 2987907000, "title": "GSM1480293: Luminal 18.5 dP #1; Mus musculus; RNA-Seq", "resolves": true}, {"run": "SRR1552447", "sample": "GSM1480294", "cell_type": "L", "status": "pregnant", "experiment": "SRX681988", "total_spots": 29245388, "total_bases": 2924538800, "title": "GSM1480294: Luminal 18.5 dP #2; Mus musculus; RNA-Seq", "resolves": true}, {"run": "SRR1552448", "sample": "GSM1480295", "cell_type": "L", "status": "lactating", "experiment": "SRX681989", "total_spots": 31425424, "total_bases": 3142542400, "title": "GSM1480295: Luminal 2 dL #1; Mus musculus; RNA-Seq", "resolves": true}, {"run": "SRR1552449", "sample": "GSM1480296", "cell_type": "L", "status": "lactating", "experiment": "SRX681990", "total_spots": 31276061, "total_bases": 3127606100, "title": "GSM1480296: Luminal 2 dL #2; Mus musculus; RNA-Seq", "resolves": true}], "runs_resolved": 12, "access_route": "the SRA accession URL, or fastq-dump", "downloaded": false, "licence_read": false, "licence": "No licence statement is given in the repository record."}}, {"id": "data:geo:GSE60450-counts", "role": "supplementary", "format": "geo-supplementary", "media_type": "text/tab-values", "uri": "https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE60450&format=file&file=GSE60450_Lactation-GenewiseCounts.txt.gz", "sha256": "sha256:906b6ec4c33e95ca0ba454a3e0d07ad74e9cb7528ee38b89a9b122f5674a5f0d", "bytes": 513592, "access": "open", "state": "verified", "reader": null, "reader_status": "available", "identifier": "GSE60450_Lactation-GenewiseCounts.txt.gz", "version": null, "note": "The genewise read-count matrix the paper analyses: 27179 genes over twelve libraries, named by the repository. Fetched and hashed on 4 November 2026, and checked against the numbers the paper printed.", "structure": {"repository": "GEO", "series": "GSE60450", "access_route": "the GEO download URL", "downloaded": true, "fetched_at": "2026-11-04", "licence_read": false, "licence": "No licence statement is given in the repository record.", "verification": {"checked_on": "2026-11-04", "method": "The counts in the fetched file were summed per library and compared with the lib.size the paper printed. The annotation the paper's sessionInfo names was fetched from the Bioconductor 3.3 archive, the genes without a symbol were dropped as the paper drops them, and the paper's filter was applied to what was left.", "library_totals": {"agrees": true, "detail": "All twelve library totals equal the lib.size printed in section 4, from MCL1.DG 23227641 to MCL1.LF 24657293, so every row of the fetched file is accounted for."}, "annotation": {"agrees": true, "detail": "822 of the 27179 genes carry no symbol in org.Mm.eg.db 3.3.0, leaving 26357, which is the dimension the paper prints after the drop."}, "filter": {"agrees": true, "detail": "The rule as the paper writes it - counts per million above 0.5 in at least two libraries, over the library sizes the paper printed - keeps 15653 genes and discards 10704, and all twelve post-filter library sizes equal the lib.size printed in section 7, from MCL1.DG 23139638 to MCL1.LF 24602860."}}}}, {"id": "annotation:bioconductor:org.Mm.eg.db:3.3.0", "role": "reference", "format": "bioconductor-package", "media_type": "application/x-tar+gzip", "uri": "https://bioconductor.org/packages/3.3/data/annotation/src/contrib/org.Mm.eg.db_3.3.0.tar.gz", "sha256": "sha256:5dc93707b7ca319b295b5b19963c573d5a3817d836f458a3e30d635ddd4e2365", "bytes": 63495324, "access": "open", "state": "verified", "reader": null, "reader_status": "available", "identifier": "org.Mm.eg.db_3.3.0", "version": "3.3.0", "note": "The annotation release the paper's own sessionInfo names, fetched and hashed on 4 November 2026 from the Bioconductor 3.3 archive. It decides which genes keep a symbol, and the paper discards the ones that do not, so it is an input to the filtering stage.", "structure": {"repository": "Bioconductor", "bioconductor_release": "3.3", "package": "org.Mm.eg.db", "version": "3.3.0", "access_route": "the Bioconductor archive URL", "fetched_at": "2026-11-04", "organism": "Mus musculus", "entrez_ids_with_a_symbol": 69029, "licence": "The package states no licence; the archive is public."}}, {"id": "code:wehi:targets.txt", "role": "code", "format": "text/plain", "media_type": "text/plain", "uri": "http://bioinf.wehi.edu.au/edgeR/F1000Research2016/targets.txt", "sha256": "sha256:88ae42c0539403073f0bbbd53287dd9c9cf61ddd5b1a42856243d7d99113cb8b", "bytes": 525, "access": "open", "state": "verified", "reader": null, "reader_status": "available", "identifier": "targets.txt", "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": "code:wehi:edgeRQL.R", "role": "code", "format": "R source", "media_type": "text/x-r-source", "uri": "http://bioinf.wehi.edu.au/edgeR/F1000Research2016/edgeRQL.R", "sha256": "sha256:3b11478ac314c4456af8b4ba7af7992e938488ffc7bec88d3f73f42aed4c0bba", "bytes": 10298, "access": "open", "state": "verified", "reader": null, "reader_status": "available", "identifier": "edgeRQL.R", "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": "code:wehi:edgeRQL.Rnw", "role": "code", "format": "Rnw source", "media_type": "text/x-tex", "uri": "http://bioinf.wehi.edu.au/edgeR/F1000Research2016/edgeRQL.Rnw", "sha256": "sha256:defd3acb73dcbfe885ca02209ac9437b785b4ccf12c7ba09a8a8bb311173902d", "bytes": 59373, "access": "open", "state": "verified", "reader": null, "reader_status": "available", "identifier": "edgeRQL.Rnw", "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": "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", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-03T19:28:53Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 141056, "completion_tokens": 5542, "cached_tokens": 34816}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:27508061", "type": "paper", "label": "pmid:27508061"}, {"id": "source:pmid:27508061", "type": "manuscript", "label": "PMID 27508061 full text"}, {"id": "data:geo:GSE60450", "type": "dataset", "label": "GEO GSE60450"}], "activities": [{"id": "activity-sci-assay-array-2026-11-03", "type": "classification", "used": [{"id": "pmid:27508061", "type": "paper", "label": "pmid:27508061"}, {"id": "source:pmid:27508061", "type": "manuscript", "label": "PMID 27508061 full text"}, {"id": "data:geo:GSE60450", "type": "dataset", "label": "GEO GSE60450"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-27508061", "type": "extraction", "used": ["source:pmid:27508061"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE60450", "type": "accession_resolution", "used": ["data:geo:GSE60450"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"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": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"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", "definition_digest": "sha256:781215e3b5e462988c0f0a214b7462f32b5e18c58a59ff0e7366fdf7059c67a9", "required_operations": ["rna_seq_read_alignment"], "support_state": "unsupported", "source_hashes": {"assay_definition": "sha256:096fe08e9f4c2a4cf0c344fce05384c3be6b532af00f0ebb651aeb690f0e1a45", "assay_definition_digest": "sha256:781215e3b5e462988c0f0a214b7462f32b5e18c58a59ff0e7366fdf7059c67a9", "corpus_definition_alias": "c3654ea6-862a-401b-8561-f5fd9b278ded", "dsl_catalogue": "f2132e96ae6c7a4e", "source_text": "3bf8a3f4c0135bde16e66f7f232937e6a89868783968461f69da3b9c8795dceb"}, "confidence": 1.0, "evidence": ["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.", "The sequence reads can now be aligned to the mouse genome using the align function:"], "order_basis": "paper_text_order:19240", "depends_on": [], "operations": [], "id": "assay:1"}, {"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": "rna-seq-count-filtering-and-normalisation", "definition_version": "0.1.0", "definition_digest": "sha256:029f48150fdbe3973df58cc1d9a63ea34bd5ba35c319469ee1cfd1249101c0fe", "required_operations": ["normalise_counts", "normalise_counts_tmm"], "support_state": "partial", "source_hashes": {"assay_definition": "sha256:e6870140eb683be699faca0423dc8601c085f696ba651a94bfe9bdee05489106", "assay_definition_digest": "sha256:029f48150fdbe3973df58cc1d9a63ea34bd5ba35c319469ee1cfd1249101c0fe", "corpus_definition_alias": "9acecdb9-4411-49af-9388-c808263d7e16", "dsl_catalogue": "f2132e96ae6c7a4e", "source_text": "3bf8a3f4c0135bde16e66f7f232937e6a89868783968461f69da3b9c8795dceb"}, "confidence": 1.0, "evidence": ["For the current analysis, we keep genes that have CPM values above 0.5 in at least two libraries:", "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": ["assay:2"], "operations": [{"operation": "normalise_counts", "support_state": "partial", "input_contract": {"fields": ["counts_per_million", "deterministic", "library_sizes", "log_counts", "n_genes", "n_samples"]}, "limitations": ["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"}, {"role": "analysis", "definition_id": "rna-seq-differential-expression", "definition_version": "0.1.0", "definition_digest": "sha256:dfda866165c72d6cd1517a23e85867cdaa0adc1df88f9977b642792bdcdc7278", "required_operations": ["differential_expression_fit", "fdr_bh", "differential_expression_quasi_likelihood"], "support_state": "partial", "source_hashes": {"assay_definition": "sha256:47bf2e85188384fddc7d6f5218de96a59230ad1577d39b8cb0c0e161275885b2", "assay_definition_digest": "sha256:dfda866165c72d6cd1517a23e85867cdaa0adc1df88f9977b642792bdcdc7278", "corpus_definition_alias": "bb104c14-fd8c-4c39-a3cd-be17740ca6f7", "dsl_catalogue": "f2132e96ae6c7a4e", "source_text": "3bf8a3f4c0135bde16e66f7f232937e6a89868783968461f69da3b9c8795dceb"}, "confidence": 1.0, "evidence": ["The workflow uses edgeR’s quasi-likelihood pipeline (edgeR-quasi) for differential expression.", "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:", "In edgeR, this can be done using the glmTreat function."], "order_basis": "consumes_earlier_output", "depends_on": ["assay:3"], "operations": [{"operation": "differential_expression_fit", "support_state": "partial", "input_contract": {"fields": ["deterministic", "genes", "n_control", "n_genes", "n_treatment"]}, "limitations": ["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."}, {"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). 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": ["assay:4"], "operations": [{"operation": "pathway_enrich", "support_state": "supported", "input_contract": {"fields": ["background_size", "deterministic", "hit_size", "pathways"]}, "limitations": ["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"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-04T14:24:55+00:00","generated_at":"2026-11-04T18:29:14+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}