Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:41158841

Integrated Expression Analysis May Support Serine/Threonine Kinases as Common Hub Genes in Breast Cancer.

Iranian journal of medical sciences · 2025 doi:10.30476/ijms.2025.104386.3798

Paper

partial

Experiment

partial

Data

partial

Analysis

absent

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:41158841
kind
science-record
content_hash
sha256:15b7f1b06f56f15d201404ebad19f4a5ddd9c85511a7c81a009afdc39c735920
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T10:25:53Z
updated_at
2026-11-01T14:01:50Z
generator object · 3 fields
name
corpus-assay-engine
converter
sep_to_sci_v1
source_package_schema
urn:bntrg:sep:1.0.0
paper object · 10 fields
state
partial
title
Integrated Expression Analysis May Support Serine/Threonine Kinases as Common Hub Genes in Breast Cancer.
doi
10.30476/ijms.2025.104386.3798
pmid
41158841
authors
null
journal
Iranian journal of medical sciences
year
2025
abstract
null
claims array · 1 item
[0] object · 6 fields
id
claim-1
statement
the headline numerical result the paper states for its main finding
kind
qualitative
state
blocked
target object · 4 fields
value
null
unit
null
tolerance
null
source
null
evidence array · 0 items
gaps array · 2 items
[0]
abstract
[1]
authors
experiment object · 8 fields
state
partial
objective
the headline numerical result the paper states for its main finding
steps array · 3 items
[0] object · 13 fields
id
read_published_estimate
order
1
name
Read the published estimate and its interval from the source
kind
other
state
complete
blocked_on
null
description
The number a replication must land on, and the sentence it came from.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:41158841
outputs array · 1 item
[0]
the published estimate, its unit and its interval
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data behind the published result
kind
data-preparation
state
blocked
blocked_on
data:not_downloaded
description
The published result cannot be recomputed without the data the paper analysed.
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the source data with its provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
id
run_analysis
order
3
name
Run the analysis programme
kind
analysis
state
blocked
blocked_on
no owned computational capability is bound to this experiment
description
Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:41158841
parameters object · 0 fields
inputs array · 0 items
outputs array · 1 item
[0]
the registered result
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 3 items
[0]
step:obtain_source_data blocked on data:not_downloaded
[1]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[2]
step:run_analysis input 'materials:the source data behind the published result in pmid:41158841' does not resolve to a declared asset
data object · 3 fields
state
partial
assets array · 4 items
[0] object · 15 fields
id
source:pmid:41158841
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.30476/ijms.2025.104386.3798
sha256
sha256:bec4b9eb0385ec1bdea8e6c583ab95ea0454100302ac895bf3f703963d6e700c
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.30476/ijms.2025.104386.3798
version
null
note
Source read by the package builder: full_text.
structure object · 1 field
access_state
full_text
[1] object · 16 fields
id
asset:table:pmid:41158841:1
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:4eb2fa26369a8752e779051450407c77af0d7310c6f0a62166a13d2544b78a35
bytes
1047
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[7]/table-wrap[1]#T1
version
null
note
Detailed information on the studies included in this analysis.
structure object · 5 fields
pmcid
PMC12557343
section_index
7
section_title
Datasets
row_count
5
column_count
5
table object · 8 fields
label
Table 1
caption
Detailed information on the studies included in this analysis.
rows array · 5 items
[0] array · 5 items
[0]
GSE No.
[1]
Study
[2]
Number of samples
[3]
Platform
[4]
Organism
[1] array · 5 items
[0]
GSE161533
[1]
Expression data from esophageal squamous cell carcinoma patients 27
[2]
84
[3]
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
[4]
Homo sapiens
[2] array · 5 items
[0]
GSE162228
[1]
Concordance of PAM50 molecular subtyping between oligonucleotide microarray and NanoString nCounter assay for Taiwanese BC 28
[2]
133
[3]
[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
[4]
Homo sapiens
[3] array · 5 items
[0]
GSE70947
[1]
Age and estrogen-dependent inflammation in breast adenocarcinoma and normal breast tissue [cohort_2] 29
[2]
296
[3]
Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Feature Number version)
[4]
Homo sapiens
[4] array · 5 items
[0]
GSE139038
[1]
Gene expression profiling in paired normal, apparently normal, and breast tumor tissues 30
[2]
65
[3]
Print_1437(Block_Column_Row IDs)
[4]
Homo sapiens
locator
section[7]/table-wrap[1]#T1
[2] object · 16 fields
id
asset:table:pmid:41158841:2
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:14cf67364d16c5ed12ee01e580ed0d0876344e678a8cb49a764cda1c3df7c9fe
bytes
1052
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[16]/table-wrap[1]#T2
version
null
note
Significantly enriched examination of the identification of differentially expressed genes in control samples in the KEGG pathway
structure object · 5 fields
pmcid
PMC12557343
section_index
16
section_title
Hub Gene Ontology Analysis in BC
row_count
11
column_count
4
table object · 8 fields
label
Table 2
caption
Significantly enriched examination of the identification of differentially expressed genes in control samples in the KEGG pathway
rows array · 11 items
[0] array · 4 items
[0]
Term
[1]
P value
[2]
Adj. P value
[3]
Genes
[1] array · 4 items
[0]
Cell cycle
[1]
4.14E-10
[2]
7.86E-09
[3]
CCNB1; CHEK1; PLK1; BUB1B; MCM4; MAD2L1; MCM2
[2] array · 4 items
[0]
Progesterone-mediated oocyte maturation
[1]
4.03E-04
[2]
0.0038306
[3]
CCNB1; PLK1; MAD2L1
[3] array · 4 items
[0]
Oocyte meiosis
[1]
8.47E-04
[2]
0.005089732
[3]
CCNB1; PLK1; MAD2L1
[4] array · 4 items
[0]
DNA replication
[1]
0.0012404
[2]
0.005089732
[3]
MCM4; MCM2
[5] array · 4 items
[0]
Cellular senescence
[1]
0.0014656
[2]
0.005089732
[3]
CCNB1; CHEK1; MYBL2
[6] array · 4 items
[0]
Homologous recombination
[1]
0.0016073
[2]
0.005089732
[3]
BLM; RAD51
[7] array · 4 items
[0]
Fanconi anemia pathway
[1]
0.0027724
[2]
0.007525035
[3]
BLM; RAD51
[8] array · 4 items
[0]
Human T-cell leukemia virus 1 infection
[1]
0.0038357
[2]
0.009109689
[3]
CHEK1; BUB1B; MAD2L1
[9] array · 4 items
[0]
p53 signaling pathway
[1]
0.0050055
[2]
0.010567085
[3]
CCNB1; CHEK1
[10] array · 4 items
[0]
FoxO signaling pathway
[1]
0.0153991
[2]
0.029258385
[3]
CCNB1; PLK1
locator
section[16]/table-wrap[1]#T2
[3] object · 16 fields
id
asset:table:pmid:41158841:3
role
table
format
jats-table
media_type
application/vnd.jats.table+json
uri
null
sha256
sha256:9c6ca913cc92731cb1eb4828960a716a9c4086f4f146079385f5f7e54eea76b4
bytes
1391
access
open
state
verified
reader
read_table
reader_status
available
identifier
section[16]/table-wrap[2]#T3
version
null
note
The enrichment of DEGs in BC in the KEGG pathway (Top 15 according to P value)
structure object · 5 fields
pmcid
PMC12557343
section_index
16
section_title
Hub Gene Ontology Analysis in BC
row_count
11
column_count
4
table object · 8 fields
label
Table 3
caption
The enrichment of DEGs in BC in the KEGG pathway (Top 15 according to P value)
rows array · 11 items
[0] array · 4 items
[0]
Term
[1]
P value
[2]
Adj. P value
[3]
Genes
[1] array · 4 items
[0]
Pathways in cancer
[1]
1.12E-16
[2]
2.11E-14
[3]
PDGFRB; EDN1; SMAD3; HSP90AB1; HDAC1; HGF; PTEN; EGFR; CXCL12; AKT1; CTNNB1; PPARG; TP53; HRAS
[2] array · 4 items
[0]
Prostate cancer
[1]
1.25E-15
[2]
1.10E-13
[3]
PDGFRB; HSP90AB1; PTEN; AKT1; CTNNB1; TP53; HRAS; EGFR; INS
[3] array · 4 items
[0]
PI3K-Akt signaling pathway
[1]
1.75E-15
[2]
1.10E-13
[3]
PDGFRB; HSP90AB1; CSF1; NOS3; HGF; PTEN; AKT1; TP53; HRAS; TLR4; EGFR; INS
[4] array · 4 items
[0]
Proteoglycans in cancer
[1]
1.78E-14
[2]
8.35E-13
[3]
SRC; HGF; AKT1; CTNNB1; TNF; TP53; HRAS; TLR4; EGFR; ACTB
[5] array · 4 items
[0]
Rap1 signaling pathway
[1]
2.27E-14
[2]
8.52E-13
[3]
PDGFRB; CSF1; SRC; HGF; AKT1; CTNNB1; HRAS; EGFR; ACTB; INS
[6] array · 4 items
[0]
Lipid and atherosclerosis
[1]
2.87E-14
[2]
9.00E-13
[3]
CD40; HSP90AB1; SRC; NOS3; AKT1; PPARG; TNF; TP53; HRAS; TLR4
[7] array · 4 items
[0]
Fluid shear stress and atherosclerosis
[1]
3.48E-14
[2]
9.35E-13
[3]
EDN1; HSP90AB1; SRC; NOS3; AKT1; CTNNB1; TNF; TP53; ACTB
[8] array · 4 items
[0]
Hepatocellular carcinoma
[1]
1.97E-13
[2]
4.63E-12
[3]
SMAD3; HGF; PTEN; AKT1; CTNNB1; TP53; HRAS; EGFR; ACTB
[9] array · 4 items
[0]
Focal adhesion
[1]
1.00E-12
[2]
2.09E-11
[3]
PDGFRB; SRC; HGF; PTEN; AKT1; CTNNB1; HRAS; EGFR; ACTB
[10] array · 4 items
[0]
Melanoma
[1]
1.91E-12
[2]
3.60E-11
[3]
PDGFRB; HGF; PTEN; AKT1; TP53; HRAS; EGFR
locator
section[16]/table-wrap[2]#T3
gaps array · 1 item
[0]
asset:source:pmid:41158841 not verified
analysis object · 4 fields
state
absent
methods array · 0 items
targets array · 0 items
gaps array · 2 items
[0]
method
[1]
targets
capability object · 3 fields
state
absent
requirements array · 0 items
gaps array · 1 item
[0]
capability
readiness object · 8 fields
state
partial
tier
null
blocked_on
null
axes object · 0 fields
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 4 items
[0]
source:pmid:41158841
[1]
asset:table:pmid:41158841:1
[2]
asset:table:pmid:41158841:2
[3]
asset:table:pmid:41158841:3
steps array · 1 item
[0]
read_published_estimate
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 1 item
[0]
xml
capabilities array · 0 items
data_gaps array · 1 item
[0]
source:pmid:41158841
gaps array · 1 item
[0]
corpus_record_absent
review object · 5 fields
state
partial
machine_critique object · 7 fields
status
blocked
providers array · 0 items
target_providers array · 0 items
agreement
false
disagreements array · 0 items
agreement_basis object · 2 fields
policy
decisive_fields
decisive_fields array · 4 items
[0]
work_type
[1]
number_stated
[2]
parent_value
[3]
unit
blinded
true
human_critique object · 5 fields
status
not_run
reviewer
null
signed_at
null
conflict_checked
false
commentary
null
stages array · 7 items
[0] object · 4 fields
key
target_materials
status
pending
reason
null
evidence
null
[1] object · 4 fields
key
independent_readings
status
blocked
reason
The independent readings are incomplete or disagree; the source evidence must resolve the difference.
evidence object · 1 field
provider_errors array · 4 items
[0] object · 4 fields
provider
minimax
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[1] object · 4 fields
provider
minimax_alt
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[2] object · 4 fields
provider
minimax
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[3] object · 4 fields
provider
minimax_alt
model
null
reason
HTTP Error 429: Too Many Requests
raw_response
null
[2] object · 4 fields
key
source_resolution
status
pending
reason
null
evidence
null
[3] object · 4 fields
key
protocol_reconstruction
status
pending
reason
null
evidence
null
[4] object · 4 fields
key
control_execution
status
pending
reason
null
evidence
null
[5] object · 4 fields
key
control_comparison
status
pending
reason
null
evidence
null
[6] object · 4 fields
key
publication
status
pending
reason
null
evidence
null
gaps array · 3 items
[0]
review.human_critique
[1]
review.machine_critique.blocked
[2]
review.machine_critique.providers
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 1 item
[0] object · 3 fields
id
package:07da1b2a025cb633e5c8de4d1839567c7749c5af238cc8f40f433bf0bd07ca2a
type
sep_package
label
SEP v1 package for pmid:41158841
activities array · 1 item
[0] object · 4 fields
id
activity:conversion:pmid:41158841
type
conversion
used array · 1 item
[0]
package:07da1b2a025cb633e5c8de4d1839567c7749c5af238cc8f40f433bf0bd07ca2a
agent
agent:corpus-assay-engine
agents array · 1 item
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
source_run_id
run-20261023T122449232913
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:41158841
parent_hash
sha256:d71e8a33f58c645524c52700d1059dc4a2d768705693e96bea06cc1a77350b3e
fork_of
null
gaps array · 14 items
[0]
abstract
[1]
asset:source:pmid:41158841 not verified
[2]
authors
[3]
capability
[4]
corpus_record_absent
[5]
execution.not_run
[6]
method
[7]
review.human_critique
[8]
review.machine_critique.blocked
[9]
review.machine_critique.providers
[10]
step:obtain_source_data blocked on data:not_downloaded
[11]
step:run_analysis blocked on no owned computational capability is bound to this experiment
[12]
step:run_analysis input 'materials:the source data behind the published result in pmid:41158841' does not resolve to a declared asset
[13]
targets
Complete file
{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41158841", "kind": "science-record", "revision": 2, "content_hash": "sha256:15b7f1b06f56f15d201404ebad19f4a5ddd9c85511a7c81a009afdc39c735920", "created_at": "2026-11-01T10:25:53Z", "updated_at": "2026-11-01T14:01:50Z", "generator": {"name": "corpus-assay-engine", "converter": "sep_to_sci_v1", "source_package_schema": "urn:bntrg:sep:1.0.0"}, "paper": {"state": "partial", "title": "Integrated Expression Analysis May Support Serine/Threonine Kinases as Common Hub Genes in Breast Cancer.", "doi": "10.30476/ijms.2025.104386.3798", "pmid": "41158841", "authors": null, "journal": "Iranian journal of medical sciences", "year": 2025, "abstract": null, "claims": [{"id": "claim-1", "statement": "the headline numerical result the paper states for its main finding", "kind": "qualitative", "state": "blocked", "target": {"value": null, "unit": null, "tolerance": null, "source": null}, "evidence": []}], "gaps": ["abstract", "authors"]}, "experiment": {"state": "partial", "objective": "the headline numerical result the paper states for its main finding", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate and its interval from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The number a replication must land on, and the sentence it came from.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:41158841"], "outputs": ["the published estimate, its unit and its interval"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data behind the published result", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:not_downloaded", "description": "The published result cannot be recomputed without the data the paper analysed.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the analysis programme", "kind": "analysis", "state": "blocked", "blocked_on": "no owned computational capability is bound to this experiment", "description": "Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:41158841", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the registered result"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:41158841' does not resolve to a declared asset"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41158841", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.30476/ijms.2025.104386.3798", "sha256": "sha256:bec4b9eb0385ec1bdea8e6c583ab95ea0454100302ac895bf3f703963d6e700c", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.30476/ijms.2025.104386.3798", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:41158841:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4eb2fa26369a8752e779051450407c77af0d7310c6f0a62166a13d2544b78a35", "bytes": 1047, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[7]/table-wrap[1]#T1", "version": null, "note": "Detailed information on the studies included in this analysis.", "structure": {"pmcid": "PMC12557343", "section_index": 7, "section_title": "Datasets", "row_count": 5, "column_count": 5}, "table": {"label": "Table 1", "caption": "Detailed information on the studies included in this analysis.", "rows": [["GSE No.", "Study", "Number of samples", "Platform", "Organism"], ["GSE161533", "Expression data from esophageal squamous cell carcinoma patients 27", "84", "[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array", "Homo sapiens"], ["GSE162228", "Concordance of PAM50 molecular subtyping between oligonucleotide microarray and NanoString nCounter assay for Taiwanese BC 28", "133", "[HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array", "Homo sapiens"], ["GSE70947", "Age and estrogen-dependent inflammation in breast adenocarcinoma and normal breast tissue [cohort_2] 29", "296", "Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Feature Number version)", "Homo sapiens"], ["GSE139038", "Gene expression profiling in paired normal, apparently normal, and breast tumor tissues 30", "65", "Print_1437(Block_Column_Row IDs)", "Homo sapiens"]], "row_count": 5, "column_count": 5, "numeric_cells": 16, "header_rows": 1, "locator": "section[7]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:41158841:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:14cf67364d16c5ed12ee01e580ed0d0876344e678a8cb49a764cda1c3df7c9fe", "bytes": 1052, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#T2", "version": null, "note": "Significantly enriched examination of the identification of differentially expressed genes in control samples in the KEGG pathway", "structure": {"pmcid": "PMC12557343", "section_index": 16, "section_title": "Hub Gene Ontology Analysis in BC", "row_count": 11, "column_count": 4}, "table": {"label": "Table 2", "caption": "Significantly enriched examination of the identification of differentially expressed genes in control samples in the KEGG pathway", "rows": [["Term", "P value", "Adj. P value", "Genes"], ["Cell cycle", "4.14E-10", "7.86E-09", "CCNB1; CHEK1; PLK1; BUB1B; MCM4; MAD2L1; MCM2"], ["Progesterone-mediated oocyte maturation", "4.03E-04", "0.0038306", "CCNB1; PLK1; MAD2L1"], ["Oocyte meiosis", "8.47E-04", "0.005089732", "CCNB1; PLK1; MAD2L1"], ["DNA replication", "0.0012404", "0.005089732", "MCM4; MCM2"], ["Cellular senescence", "0.0014656", "0.005089732", "CCNB1; CHEK1; MYBL2"], ["Homologous recombination", "0.0016073", "0.005089732", "BLM; RAD51"], ["Fanconi anemia pathway", "0.0027724", "0.007525035", "BLM; RAD51"], ["Human T-cell leukemia virus 1 infection", "0.0038357", "0.009109689", "CHEK1; BUB1B; MAD2L1"], ["p53 signaling pathway", "0.0050055", "0.010567085", "CCNB1; CHEK1"], ["FoxO signaling pathway", "0.0153991", "0.029258385", "CCNB1; PLK1"]], "row_count": 11, "column_count": 4, "numeric_cells": 24, "header_rows": 1, "locator": "section[16]/table-wrap[1]#T2"}}, {"id": "asset:table:pmid:41158841:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9c6ca913cc92731cb1eb4828960a716a9c4086f4f146079385f5f7e54eea76b4", "bytes": 1391, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[2]#T3", "version": null, "note": "The enrichment of DEGs in BC in the KEGG pathway (Top 15 according to P value)", "structure": {"pmcid": "PMC12557343", "section_index": 16, "section_title": "Hub Gene Ontology Analysis in BC", "row_count": 11, "column_count": 4}, "table": {"label": "Table 3", "caption": "The enrichment of DEGs in BC in the KEGG pathway (Top 15 according to P value)", "rows": [["Term", "P value", "Adj. P value", "Genes"], ["Pathways in cancer", "1.12E-16", "2.11E-14", "PDGFRB; EDN1; SMAD3; HSP90AB1; HDAC1; HGF; PTEN; EGFR; CXCL12; AKT1; CTNNB1; PPARG; TP53; HRAS"], ["Prostate cancer", "1.25E-15", "1.10E-13", "PDGFRB; HSP90AB1; PTEN; AKT1; CTNNB1; TP53; HRAS; EGFR; INS"], ["PI3K-Akt signaling pathway", "1.75E-15", "1.10E-13", "PDGFRB; HSP90AB1; CSF1; NOS3; HGF; PTEN; AKT1; TP53; HRAS; TLR4; EGFR; INS"], ["Proteoglycans in cancer", "1.78E-14", "8.35E-13", "SRC; HGF; AKT1; CTNNB1; TNF; TP53; HRAS; TLR4; EGFR; ACTB"], ["Rap1 signaling pathway", "2.27E-14", "8.52E-13", "PDGFRB; CSF1; SRC; HGF; AKT1; CTNNB1; HRAS; EGFR; ACTB; INS"], ["Lipid and atherosclerosis", "2.87E-14", "9.00E-13", "CD40; HSP90AB1; SRC; NOS3; AKT1; PPARG; TNF; TP53; HRAS; TLR4"], ["Fluid shear stress and atherosclerosis", "3.48E-14", "9.35E-13", "EDN1; HSP90AB1; SRC; NOS3; AKT1; CTNNB1; TNF; TP53; ACTB"], ["Hepatocellular carcinoma", "1.97E-13", "4.63E-12", "SMAD3; HGF; PTEN; AKT1; CTNNB1; TP53; HRAS; EGFR; ACTB"], ["Focal adhesion", "1.00E-12", "2.09E-11", "PDGFRB; SRC; HGF; PTEN; AKT1; CTNNB1; HRAS; EGFR; ACTB"], ["Melanoma", "1.91E-12", "3.60E-11", "PDGFRB; HGF; PTEN; AKT1; TP53; HRAS; EGFR"]], "row_count": 11, "column_count": 4, "numeric_cells": 28, "header_rows": 1, "locator": "section[16]/table-wrap[2]#T3"}}], "gaps": ["asset:source:pmid:41158841 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:41158841", "asset:table:pmid:41158841:1", "asset:table:pmid:41158841:2", "asset:table:pmid:41158841:3"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:41158841"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [], "target_providers": [], "agreement": false, "disagreements": [], "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": [{"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}, {"provider": "minimax_alt", "model": null, "reason": "HTTP Error 429: Too Many Requests", "raw_response": null}]}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:07da1b2a025cb633e5c8de4d1839567c7749c5af238cc8f40f433bf0bd07ca2a", "type": "sep_package", "label": "SEP v1 package for pmid:41158841"}], "activities": [{"id": "activity:conversion:pmid:41158841", "type": "conversion", "used": ["package:07da1b2a025cb633e5c8de4d1839567c7749c5af238cc8f40f433bf0bd07ca2a"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:41158841", "parent_hash": "sha256:d71e8a33f58c645524c52700d1059dc4a2d768705693e96bea06cc1a77350b3e", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:41158841 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "review.machine_critique.providers", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:41158841' does not resolve to a declared asset", "targets"]}