← All .science files
pmid:29344121
A five-gene based risk score with high prognostic value in colorectal cancer.
Yida Pan · Hongyang Zhang · Mingming Zhang · Jie Zhu · Jianghong Yu · Bangting Wang · Jigang Qiu · Jun Zhang
Oncology letters · 2017 doi:10.3892/ol.2017.7097
Paper
complete
Experiment
complete
Data
partial
Analysis
complete
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
paper object · 10 fields
authors array · 8 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
[2] object · 6 fields
target object · 4 fields
evidence array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
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 · 0 items
data object · 3 fields
assets array · 12 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 290 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 177 items
[3] object · 15 fields
structure object · 15 fields
sample_accessions array · 65 items
[4] object · 15 fields
structure object · 15 fields
sample_accessions array · 246 items
[5] object · 15 fields
structure object · 15 fields
sample_accessions array · 111 items
[6] object · 15 fields
structure object · 15 fields
sample_accessions array · 82 items
[7] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 24 items
[0] array · 6 items
[1] array · 6 items
[2] array · 6 items
[3] array · 6 items
[4] array · 6 items
[5] array · 6 items
[6] array · 6 items
[7] array · 6 items
[8] array · 6 items
[9] array · 6 items
[10] array · 6 items
[11] array · 6 items
[12] array · 6 items
[13] array · 6 items
[14] array · 6 items
[15] array · 6 items
[16] array · 6 items
[17] array · 6 items
[18] array · 6 items
[19] array · 6 items
[20] array · 6 items
[21] array · 6 items
[22] array · 6 items
[23] array · 6 items
[8] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 41 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[5] array · 4 items
[6] array · 4 items
[7] array · 4 items
[8] array · 4 items
[9] array · 4 items
[10] array · 4 items
[11] array · 4 items
[12] array · 4 items
[13] array · 4 items
[14] array · 4 items
[15] array · 4 items
[16] array · 4 items
[17] array · 4 items
[18] array · 4 items
[19] array · 4 items
[20] array · 4 items
[21] array · 4 items
[22] array · 4 items
[23] array · 4 items
[24] array · 4 items
[25] array · 4 items
[26] array · 4 items
[27] array · 4 items
[28] array · 4 items
[29] array · 4 items
[30] array · 4 items
[31] array · 4 items
[32] array · 4 items
[33] array · 4 items
[34] array · 4 items
[35] array · 4 items
[36] array · 4 items
[37] array · 4 items
[38] array · 4 items
[39] array · 4 items
[40] array · 4 items
[9] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 39 items
[0] array · 1 item
[1] array · 1 item
[2] array · 3 items
[3] array · 3 items
[4] array · 9 items
[5] array · 9 items
[6] array · 9 items
[7] array · 9 items
[8] array · 9 items
[9] array · 9 items
[10] array · 9 items
[11] array · 9 items
[12] array · 1 item
[13] array · 1 item
[14] array · 1 item
[15] array · 3 items
[16] array · 3 items
[17] array · 9 items
[18] array · 1 item
[19] array · 9 items
[20] array · 9 items
[21] array · 9 items
[22] array · 9 items
[23] array · 9 items
[24] array · 9 items
[25] array · 1 item
[26] array · 1 item
[27] array · 1 item
[28] array · 3 items
[29] array · 3 items
[30] array · 9 items
[31] array · 1 item
[32] array · 9 items
[33] array · 9 items
[34] array · 9 items
[35] array · 9 items
[36] array · 9 items
[37] array · 9 items
[38] array · 9 items
[10] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 41 items
[0] array · 4 items
[1] array · 4 items
[2] array · 4 items
[3] array · 4 items
[4] array · 4 items
[5] array · 4 items
[6] array · 4 items
[7] array · 4 items
[8] array · 4 items
[9] array · 4 items
[10] array · 4 items
[11] array · 4 items
[12] array · 4 items
[13] array · 4 items
[14] array · 4 items
[15] array · 4 items
[16] array · 4 items
[17] array · 4 items
[18] array · 4 items
[19] array · 4 items
[20] array · 4 items
[21] array · 4 items
[22] array · 4 items
[23] array · 4 items
[24] array · 4 items
[25] array · 4 items
[26] array · 4 items
[27] array · 4 items
[28] array · 4 items
[29] array · 4 items
[30] array · 4 items
[31] array · 4 items
[32] array · 4 items
[33] array · 4 items
[34] array · 4 items
[35] array · 4 items
[36] array · 4 items
[37] array · 4 items
[38] array · 4 items
[39] array · 4 items
[40] array · 4 items
[11] object · 16 fields
structure object · 5 fields
table object · 8 fields
rows array · 39 items
[0] array · 1 item
[1] array · 1 item
[2] array · 3 items
[3] array · 3 items
[4] array · 9 items
[5] array · 9 items
[6] array · 9 items
[7] array · 9 items
[8] array · 9 items
[9] array · 9 items
[10] array · 9 items
[11] array · 9 items
[12] array · 1 item
[13] array · 1 item
[14] array · 1 item
[15] array · 3 items
[16] array · 3 items
[17] array · 9 items
[18] array · 1 item
[19] array · 9 items
[20] array · 9 items
[21] array · 9 items
[22] array · 9 items
[23] array · 9 items
[24] array · 9 items
[25] array · 1 item
[26] array · 1 item
[27] array · 1 item
[28] array · 3 items
[29] array · 3 items
[30] array · 9 items
[31] array · 1 item
[32] array · 9 items
[33] array · 9 items
[34] array · 9 items
[35] array · 9 items
[36] array · 9 items
[37] array · 9 items
[38] array · 9 items
gaps array · 12 items
analysis object · 4 fields
methods array · 4 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[3] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 1 item
[0] object · 8 fields
gaps array · 0 items
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 6 items
resolved_accessions array · 6 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 7 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 16 items
assays array · 1 item
[0] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29344121", "kind": "science-record", "revision": 7, "content_hash": "sha256:088480e77bcec25a2f10d804ade6c3656b22fb3fc239bc48623f21ef84d1570e", "created_at": "2026-11-01T15:40:31Z", "updated_at": "2026-11-01T22:43:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A five-gene based risk score with high prognostic value in colorectal cancer.", "doi": "10.3892/ol.2017.7097", "pmid": "29344121", "authors": ["Yida Pan", "Hongyang Zhang", "Mingming Zhang", "Jie Zhu", "Jianghong Yu", "Bangting Wang", "Jigang Qiu", "Jun Zhang"], "journal": "Oncology letters", "year": 2017, "abstract": "Colorectal cancer (CRC) is one of the most frequently occurring malignancies worldwide. The outcomes of patients with similar clinical symptoms or at similar pathological stages remain unpredictable. This inherent clinical diversity is most likely due to the genetic heterogeneity. The present study aimed to create a predicting tool to evaluate patient survival based on genetic profile. Firstly, three Gene Expression Omnibus (GEO) datasets (GSE9348, GSE44076 and GSE44861) were utilized to identify and validate differentially expressed genes (DEGs) in CRC. The GSE14333 dataset containing survival information was then introduced in order to screen and verify prognosis-associated genes. Of the 66 DEGs, the present study screened out 46 biomarkers closely associated to patient overall survival. By Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, it was demonstrated that these genes participated in multiple biological processes which were highly associated with cancer proliferation, drug-resistance and metastasis, thus further affecting patient survival. The five most important genes, MET proto-oncogene, receptor tyrosine kinase, carboxypeptidase M, serine hydroxymethyltransferase 2, guanylate cyclase activator 2B and sodium voltage-gated channel a subunit 9 were selected by a random survival forests algorithm, and were further made up to a linear risk score formula by multivariable cox regression. Finally, the present study tested and verified this risk score within three independent GEO datasets (GSE14333, GSE17536 and GSE29621), and observed that patients with a high risk score had a lower overall survival (P<0.05). Furthermore, this risk score was the most significant compared with other predicting factors including age and American Joint Committee on Cancer stage, in the model, and was able to predict patient survival independently and directly. The findings suggest that this survival associated DEGs-based risk score is a powerful and accurate prognostic tool and is promisingly implemented in a clinical setting.", "claims": [{"id": "claim-method", "statement": "Survival analysis was performed by Kaplan-Meier method and Mantel-Cox log-rank test was used to evaluate the statistical significance of the differences.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29344121", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "Survival analysis was performed by Kaplan-Meier method and Mantel-Cox log-rank test was used to evaluate the statistical significance of the differences."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data which were not shown in this article could be archived by contacting the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29344121", "locator": "sections[16] \"Acknowledgements\" paragraph 2", "quote": "Data which were not shown in this article could be archived by contacting the corresponding author."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using three GEO datasets for DEG identification and validation, followed by random survival forests and multivariable Cox regression, the study identified 66 DEGs, selected five prognostic genes, and found that the resulting risk score was associated with lower overall survival in high-risk patients (P<0.05).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Finally, the present study tested and verified this risk score within three independent GEO datasets (GSE14333, GSE17536 and GSE29621), and observed that patients with a high risk score had a lower overall survival (P<0.05)."}, "evidence": [{"asset": "source:pmid:29344121", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Firstly, three Gene Expression Omnibus (GEO) datasets (GSE9348, GSE44076 and GSE44861) were utilized to identify and validate differentially expressed genes (DEGs) in CRC."}, {"asset": "source:pmid:29344121", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The five most important genes, MET proto-oncogene, receptor tyrosine kinase, carboxypeptidase M, serine hydroxymethyltransferase 2, guanylate cyclase activator 2B and sodium voltage-gated channel a subunit 9 were selected by a random survival forests algorithm, and were further made up to a linear risk score formula by multivariable cox regression."}, {"asset": "source:pmid:29344121", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Finally, the present study tested and verified this risk score within three independent GEO datasets (GSE14333, GSE17536 and GSE29621), and observed that patients with a high risk score had a lower overall survival (P<0.05)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using three GEO datasets for DEG identification and validation, followed by random survival forests and multivariable Cox regression, the study identified 66 DEGs, selected five prognostic genes, and found that the resulting risk score was associated with lower overall survival in high-risk patients (P<0.05).", "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:29344121"], "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:GSE14333"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE14333"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29344121", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/ol.2017.7097", "sha256": "sha256:03cdde83d9e567973acafe28b3de01f40ff618439f2ea2504e6bd6ba569da6be", "bytes": 30942, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3892/ol.2017.7097", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5754913", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14333", "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=GSE14333", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14333", "version": null, "note": "Data which were not shown in this article could be archived by contacting the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data which were not shown in this article could be archived by contacting the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM358341", "GSM358342", "GSM358343", "GSM358344", "GSM358345", "GSM358346", "GSM358347", "GSM358348", "GSM358349", "GSM358350", "GSM358351", "GSM358352", "GSM358353", "GSM358354", "GSM358355", "GSM358356", "GSM358357", "GSM358358", "GSM358359", "GSM358360", "GSM358361", "GSM358362", "GSM358363", "GSM358364", "GSM358365", "GSM358366", "GSM358367", "GSM358368", "GSM358369", "GSM358370", "GSM358371", "GSM358372", "GSM358373", "GSM358374", "GSM358375", "GSM358376", "GSM358377", "GSM358378", "GSM358379", "GSM358380", "GSM358381", "GSM358382", "GSM358383", "GSM358384", "GSM358385", "GSM358386", "GSM358387", "GSM358388", "GSM358389", "GSM358390", "GSM358391", "GSM358392", "GSM358393", "GSM358394", "GSM358395", "GSM358396", "GSM358397", "GSM358398", "GSM358399", "GSM358400", "GSM358401", "GSM358402", "GSM358403", "GSM358404", "GSM358405", "GSM358406", "GSM358407", "GSM358408", "GSM358409", "GSM358410", "GSM358411", "GSM358412", "GSM358413", "GSM358414", "GSM358415", "GSM358416", "GSM358417", "GSM358418", "GSM358419", "GSM358420", "GSM358421", "GSM358422", "GSM358423", "GSM358424", "GSM358425", "GSM358426", "GSM358427", "GSM358428", "GSM358429", "GSM358430", "GSM358431", "GSM358432", "GSM358433", "GSM358434", "GSM358435", "GSM358436", "GSM358437", "GSM358438", "GSM358439", "GSM358440", "GSM358441", "GSM358442", "GSM358443", "GSM358444", "GSM358445", "GSM358446", "GSM358447", "GSM358448", "GSM358449", "GSM358450", "GSM358451", "GSM358452", "GSM358453", "GSM358454", "GSM358455", "GSM358456", "GSM358457", "GSM358458", "GSM358459", "GSM358460", "GSM358461", "GSM358462", "GSM358463", "GSM358464", "GSM358465", "GSM358466", "GSM358467", "GSM358468", "GSM358469", "GSM358470", "GSM358471", "GSM358472", "GSM358473", "GSM358474", "GSM358475", "GSM358476", "GSM358477", "GSM358478", "GSM358479", "GSM358480", "GSM358481", "GSM358482", "GSM358483", "GSM358484", "GSM358485", "GSM358486", "GSM358487", "GSM358488", "GSM358489", "GSM358490", "GSM358491", "GSM358492", "GSM358493", "GSM358494", "GSM358495", "GSM358496", "GSM358497", "GSM358498", "GSM358499", "GSM358500", "GSM358501", "GSM358502", "GSM358503", "GSM358504", "GSM358505", "GSM358506", "GSM358507", "GSM358508", "GSM358509", "GSM358510", "GSM358511", "GSM358512", "GSM358513", "GSM358514", "GSM358515", "GSM358516", "GSM358517", "GSM358518", "GSM358519", "GSM358520", "GSM358521", "GSM358522", "GSM358523", "GSM358524", "GSM358525", "GSM358526", "GSM358527", "GSM358528", "GSM358529", "GSM358530", "GSM358531", "GSM358532", "GSM358533", "GSM358534", "GSM358535", "GSM358536", "GSM358537", "GSM358538", "GSM358539", "GSM358540", "GSM358541", "GSM358542", "GSM358543", "GSM358544", "GSM358545", "GSM358546", "GSM358547", "GSM358548", "GSM358549", "GSM358550", "GSM358551", "GSM358552", "GSM358553", "GSM358554", "GSM358555", "GSM358556", "GSM358557", "GSM358558", "GSM358559", "GSM358560", "GSM358561", "GSM358562", "GSM358563", "GSM358564", "GSM358565", "GSM358566", "GSM358567", "GSM358568", "GSM358569", "GSM358570", "GSM358571", "GSM358572", "GSM358573", "GSM358574", "GSM358575", "GSM358576", "GSM358577", "GSM358578", "GSM358579", "GSM358580", "GSM358581", "GSM358582", "GSM358583", "GSM358584", "GSM358585", "GSM358586", "GSM358587", "GSM358588", "GSM358589", "GSM358590", "GSM358591", "GSM358592", "GSM358593", "GSM358594", "GSM358595", "GSM358596", "GSM358597", "GSM358598", "GSM358599", "GSM358600", "GSM358601", "GSM358602", "GSM358603", "GSM358604", "GSM358605", "GSM358606", "GSM358607", "GSM358608", "GSM358609", "GSM358610", "GSM358611", "GSM358612", "GSM358613", "GSM358614", "GSM358615", "GSM358616", "GSM358617", "GSM358618", "GSM358619", "GSM358620", "GSM358621", "GSM358622", "GSM358623", "GSM358624", "GSM358625", "GSM358626", "GSM358627", "GSM358628", "GSM358629", "GSM358630"], "sample_count": 290, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from 290 primary colorectal cancers", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE17536", "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=GSE17536", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17536", "version": null, "note": "Data which were not shown in this article could be archived by contacting the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data which were not shown in this article could be archived by contacting the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM437093", "GSM437094", "GSM437095", "GSM437096", "GSM437097", "GSM437098", "GSM437099", "GSM437100", "GSM437101", "GSM437102", "GSM437103", "GSM437104", "GSM437105", "GSM437106", "GSM437107", "GSM437108", "GSM437109", "GSM437110", "GSM437111", "GSM437112", "GSM437113", "GSM437114", "GSM437115", "GSM437116", "GSM437117", "GSM437118", "GSM437119", "GSM437120", "GSM437121", "GSM437122", "GSM437123", "GSM437124", "GSM437125", "GSM437126", "GSM437127", "GSM437128", "GSM437129", "GSM437130", "GSM437131", "GSM437132", "GSM437133", "GSM437134", "GSM437135", "GSM437136", "GSM437137", "GSM437138", "GSM437139", "GSM437140", "GSM437141", "GSM437142", "GSM437143", "GSM437144", "GSM437145", "GSM437146", "GSM437147", "GSM437148", "GSM437149", "GSM437150", "GSM437151", "GSM437152", "GSM437153", "GSM437154", "GSM437155", "GSM437156", "GSM437157", "GSM437158", "GSM437159", "GSM437160", "GSM437161", "GSM437162", "GSM437163", "GSM437164", "GSM437165", "GSM437166", "GSM437167", "GSM437168", "GSM437169", "GSM437170", "GSM437171", "GSM437172", "GSM437173", "GSM437174", "GSM437175", "GSM437176", "GSM437177", "GSM437178", "GSM437179", "GSM437180", "GSM437181", "GSM437182", "GSM437183", "GSM437184", "GSM437185", "GSM437186", "GSM437187", "GSM437188", "GSM437189", "GSM437190", "GSM437191", "GSM437192", "GSM437193", "GSM437194", "GSM437195", "GSM437196", "GSM437197", "GSM437198", "GSM437199", "GSM437200", "GSM437201", "GSM437202", "GSM437203", "GSM437204", "GSM437205", "GSM437206", "GSM437207", "GSM437208", "GSM437209", "GSM437210", "GSM437211", "GSM437212", "GSM437213", "GSM437214", "GSM437215", "GSM437216", "GSM437217", "GSM437218", "GSM437219", "GSM437220", "GSM437221", "GSM437222", "GSM437223", "GSM437224", "GSM437225", "GSM437226", "GSM437227", "GSM437228", "GSM437229", "GSM437230", "GSM437231", "GSM437232", "GSM437233", "GSM437234", "GSM437235", "GSM437236", "GSM437237", "GSM437238", "GSM437239", "GSM437240", "GSM437241", "GSM437242", "GSM437243", "GSM437244", "GSM437245", "GSM437246", "GSM437247", "GSM437248", "GSM437249", "GSM437250", "GSM437251", "GSM437252", "GSM437253", "GSM437254", "GSM437255", "GSM437256", "GSM437257", "GSM437258", "GSM437259", "GSM437260", "GSM437261", "GSM437262", "GSM437263", "GSM437264", "GSM437265", "GSM437266", "GSM437267", "GSM437268", "GSM437269"], "sample_count": 177, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients (Moffitt Samples)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE29621", "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=GSE29621", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29621", "version": null, "note": "Data which were not shown in this article could be archived by contacting the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data which were not shown in this article could be archived by contacting the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM734111", "GSM734112", "GSM734113", "GSM734114", "GSM734115", "GSM734116", "GSM734117", "GSM734118", "GSM734119", "GSM734120", "GSM734121", "GSM734122", "GSM734123", "GSM734124", "GSM734125", "GSM734126", "GSM734127", "GSM734128", "GSM734129", "GSM734130", "GSM734131", "GSM734132", "GSM734133", "GSM734134", "GSM734135", "GSM734136", "GSM734137", "GSM734138", "GSM734139", "GSM734140", "GSM734141", "GSM734142", "GSM734143", "GSM734144", "GSM734145", "GSM734146", "GSM734147", "GSM734148", "GSM734149", "GSM734150", "GSM734151", "GSM734152", "GSM734153", "GSM734154", "GSM734155", "GSM734156", "GSM734157", "GSM734158", "GSM734159", "GSM734160", "GSM734161", "GSM734162", "GSM734163", "GSM734164", "GSM734165", "GSM734166", "GSM734167", "GSM734168", "GSM734169", "GSM734170", "GSM734171", "GSM734172", "GSM734173", "GSM734174", "GSM734175"], "sample_count": 65, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "mRNA and microRNA profile in colon cancer [mRNA data]", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE44076", "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=GSE44076", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE44076", "version": null, "note": "Data which were not shown in this article could be archived by contacting the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data which were not shown in this article could be archived by contacting the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1077598", "GSM1077599", "GSM1077600", "GSM1077601", "GSM1077602", "GSM1077603", "GSM1077604", "GSM1077605", "GSM1077606", "GSM1077607", "GSM1077608", "GSM1077609", "GSM1077610", "GSM1077611", "GSM1077612", "GSM1077613", "GSM1077614", "GSM1077615", "GSM1077616", "GSM1077617", "GSM1077618", "GSM1077619", "GSM1077620", "GSM1077621", "GSM1077622", "GSM1077623", "GSM1077624", "GSM1077625", "GSM1077626", "GSM1077627", "GSM1077628", "GSM1077629", "GSM1077630", "GSM1077631", "GSM1077632", "GSM1077633", "GSM1077634", "GSM1077635", "GSM1077636", "GSM1077637", "GSM1077638", "GSM1077639", "GSM1077640", "GSM1077641", "GSM1077642", "GSM1077643", "GSM1077644", "GSM1077645", "GSM1077646", "GSM1077647", "GSM1077648", "GSM1077649", "GSM1077650", "GSM1077651", "GSM1077652", "GSM1077653", "GSM1077654", "GSM1077655", "GSM1077656", "GSM1077657", "GSM1077658", "GSM1077659", "GSM1077660", "GSM1077661", "GSM1077662", "GSM1077663", "GSM1077664", "GSM1077665", "GSM1077666", "GSM1077667", "GSM1077668", "GSM1077669", "GSM1077670", "GSM1077671", "GSM1077672", "GSM1077673", "GSM1077674", "GSM1077675", "GSM1077676", "GSM1077677", "GSM1077678", "GSM1077679", "GSM1077680", "GSM1077681", "GSM1077682", "GSM1077683", "GSM1077684", "GSM1077685", "GSM1077686", "GSM1077687", "GSM1077688", "GSM1077689", "GSM1077690", "GSM1077691", "GSM1077692", "GSM1077693", "GSM1077694", "GSM1077695", "GSM1077696", "GSM1077697", "GSM1077698", "GSM1077699", "GSM1077700", "GSM1077701", "GSM1077702", "GSM1077703", "GSM1077704", "GSM1077705", "GSM1077706", "GSM1077707", "GSM1077708", "GSM1077709", "GSM1077710", "GSM1077711", "GSM1077712", "GSM1077713", "GSM1077714", "GSM1077715", "GSM1077716", "GSM1077717", "GSM1077718", "GSM1077719", "GSM1077720", "GSM1077721", "GSM1077722", "GSM1077723", "GSM1077724", "GSM1077725", "GSM1077726", "GSM1077727", "GSM1077728", "GSM1077729", "GSM1077730", "GSM1077731", "GSM1077732", "GSM1077733", "GSM1077734", "GSM1077735", "GSM1077736", "GSM1077737", "GSM1077738", "GSM1077739", "GSM1077740", "GSM1077741", "GSM1077742", "GSM1077743", "GSM1077744", "GSM1077745", "GSM1077746", "GSM1077747", "GSM1077748", "GSM1077749", "GSM1077750", "GSM1077751", "GSM1077752", "GSM1077753", "GSM1077754", "GSM1077755", "GSM1077756", "GSM1077757", "GSM1077758", "GSM1077759", "GSM1077760", "GSM1077761", "GSM1077762", "GSM1077763", "GSM1077764", "GSM1077765", "GSM1077766", "GSM1077767", "GSM1077768", "GSM1077769", "GSM1077770", "GSM1077771", "GSM1077772", "GSM1077773", "GSM1077774", "GSM1077775", "GSM1077776", "GSM1077777", "GSM1077778", "GSM1077779", "GSM1077780", "GSM1077781", "GSM1077782", "GSM1077783", "GSM1077784", "GSM1077785", "GSM1077786", "GSM1077787", "GSM1077788", "GSM1077789", "GSM1077790", "GSM1077791", "GSM1077792", "GSM1077793", "GSM1077794", "GSM1077795", "GSM1077796", "GSM1077797", "GSM1077798", "GSM1077799", "GSM1077800", "GSM1077801", "GSM1077802", "GSM1077803", "GSM1077804", "GSM1077805", "GSM1077806", "GSM1077807", "GSM1077808", "GSM1077809", "GSM1077810", "GSM1077811", "GSM1077812", "GSM1077813", "GSM1077814", "GSM1077815", "GSM1077816", "GSM1077817", "GSM1077818", "GSM1077819", "GSM1077820", "GSM1077821", "GSM1077822", "GSM1077823", "GSM1077824", "GSM1077825", "GSM1077826", "GSM1077827", "GSM1077828", "GSM1077829", "GSM1077830", "GSM1077831", "GSM1077832", "GSM1077833", "GSM1077834", "GSM1077835", "GSM1077836", "GSM1077837", "GSM1077838", "GSM1077839", "GSM1077840", "GSM1077841", "GSM1077842", "GSM1077843"], "sample_count": 246, "group_sizes": null, "group_sizes_basis": null, "platform": "13667", "taxon": "Homo sapiens", "title": "Gene expression data from healthy, adjacent normal and tumor colon cells", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE44861", "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=GSE44861", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE44861", "version": null, "note": "Data which were not shown in this article could be archived by contacting the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data which were not shown in this article could be archived by contacting the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1092909", "GSM1092910", "GSM1092911", "GSM1092912", "GSM1092913", "GSM1092914", "GSM1092915", "GSM1092916", "GSM1092917", "GSM1092918", "GSM1092919", "GSM1092920", "GSM1092921", "GSM1092922", "GSM1092923", "GSM1092924", "GSM1092925", "GSM1092926", "GSM1092927", "GSM1092928", "GSM1092929", "GSM1092930", "GSM1092931", "GSM1092932", "GSM1092933", "GSM1092934", "GSM1092935", "GSM1092936", "GSM1092937", "GSM1092938", "GSM1092939", "GSM1092940", "GSM1092941", "GSM1092942", "GSM1092943", "GSM1092944", "GSM1092945", "GSM1092946", "GSM1092947", "GSM1092948", "GSM1092949", "GSM1092950", "GSM1092951", "GSM1092952", "GSM1092953", "GSM1092954", "GSM1092955", "GSM1092956", "GSM1092957", "GSM1092958", "GSM1092959", "GSM1092960", "GSM1092961", "GSM1092962", "GSM1092963", "GSM1092964", "GSM1092965", "GSM1092966", "GSM1092967", "GSM1092968", "GSM1092969", "GSM1092970", "GSM1092971", "GSM1092972", "GSM1092973", "GSM1092974", "GSM1092975", "GSM1092976", "GSM1092977", "GSM1092978", "GSM1092979", "GSM1092980", "GSM1092981", "GSM1092982", "GSM1092983", "GSM1092984", "GSM1092985", "GSM1092986", "GSM1092987", "GSM1092988", "GSM1092989", "GSM1092990", "GSM1092991", "GSM1092992", "GSM1092993", "GSM1092994", "GSM1092995", "GSM1092996", "GSM1092997", "GSM1092998", "GSM1092999", "GSM1093000", "GSM1093001", "GSM1093002", "GSM1093003", "GSM1093004", "GSM1093005", "GSM1093006", "GSM1093007", "GSM1093008", "GSM1093009", "GSM1093010", "GSM1093011", "GSM1093012", "GSM1093013", "GSM1093014", "GSM1093015", "GSM1093016", "GSM1093017", "GSM1093018", "GSM1093019"], "sample_count": 111, "group_sizes": null, "group_sizes_basis": null, "platform": "3921", "taxon": "Homo sapiens", "title": "Affymetrix expression data from colon cancer patient tissues", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE9348", "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=GSE9348", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE9348", "version": null, "note": "Data which were not shown in this article could be archived by contacting the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data which were not shown in this article could be archived by contacting the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM237914", "GSM237915", "GSM237916", "GSM237917", "GSM237918", "GSM237919", "GSM237920", "GSM237921", "GSM237922", "GSM237923", "GSM237924", "GSM237925", "GSM237926", "GSM237927", "GSM237928", "GSM237929", "GSM237930", "GSM237931", "GSM237932", "GSM237933", "GSM237934", "GSM237935", "GSM237936", "GSM237937", "GSM237938", "GSM237939", "GSM237940", "GSM237941", "GSM237942", "GSM237943", "GSM237944", "GSM237945", "GSM237946", "GSM237947", "GSM237948", "GSM237949", "GSM237950", "GSM237951", "GSM237952", "GSM237953", "GSM237954", "GSM237955", "GSM237956", "GSM237957", "GSM237958", "GSM237959", "GSM237960", "GSM237961", "GSM237962", "GSM237963", "GSM237964", "GSM237965", "GSM237966", "GSM237967", "GSM237968", "GSM237969", "GSM237970", "GSM237971", "GSM237972", "GSM237973", "GSM237974", "GSM237975", "GSM237976", "GSM237977", "GSM237978", "GSM237979", "GSM237980", "GSM237981", "GSM237982", "GSM237983", "GSM237984", "GSM237985", "GSM237986", "GSM237987", "GSM237988", "GSM237989", "GSM237990", "GSM237991", "GSM237992", "GSM237993", "GSM237994", "GSM237995"], "sample_count": 82, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from healthy controls and early stage CRC patient's tumor", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:29344121:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:3ca17d26e464584451e45d47e4a7743adb6dbd72be0b1a35a68326db82679d50", "bytes": 1527, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#tI-ol-0-0-7097", "version": null, "note": "Survival related DEGs by univariable cox proportional hazards regression analysis.", "structure": {"pmcid": "PMC5754913", "section_index": 10, "section_title": "Identification of DEGs between cancerous and non-cancerous tissues", "row_count": 24, "column_count": 6}, "table": {"label": "Table I.", "caption": "Survival related DEGs by univariable cox proportional hazards regression analysis.", "rows": [["Gene", "P-value", "HR", "Gene", "P-value", "HR"], ["LOC339166", "<1e-07", "7.748", "MYC", "7E-07", "0.581"], ["SCN9A", "<1e-07", "0.154", "SQRDL", "7E-07", "0.513"], ["LGI1", "<1e-07", "0.115", "SHMT2", "0.000001", "0.509"], ["P2RY1", "<1e-07", "3.592", "PDE6A", "2.1E-06", "2.229"], ["PRPF4", "<1e-07", "0.245", "UGDH", "2.3E-06", "1.792"], ["GUCA2B", "<1e-07", "1.688", "PTPRH", "2.5E-06", "1.733"], ["ENOX2", "<1e-07", "0.193", "PPP2R3A", "8.4E-06", "2.19"], ["NPY", "<1e-07", "4.787", "HSPH1", "2.62E-05", "1.61"], ["SCGN", "<1e-07", "2.266", "NR5A2", "3.16E-05", "0.585"], ["TMEM9B", "<1e-07", "3.445", "TRIP13", "3.21E-05", "0.631"], ["RNASEH2A", "<1e-07", "0.438", "CPM", "6.06E-05", "0.498"], ["HSD11B2", "<1e-07", "0.647", "DUSP14", "0.000183", "0.54"], ["DENND2A", "<1e-07", "0.299", "RCL1", "0.000274", "0.415"], ["ASPA", "<1e-07", "3.507", "ETV4", "0.000396", "0.672"], ["CA7", "<1e-07", "2.626", "SEMA6D", "0.000472", "1.9"], ["LPHN3", "<1e-07", "0.247", "HOMER1", "0.000475", "0.666"], ["ABCG2", "<1e-07", "1.497", "CCND1", "0.000522", "1.584"], ["GALNT6", "<1e-07", "0.588", "METTL7A", "0.000543", "2.012"], ["PTGDR", "<1e-07", "0.336", "MET", "0.000577", "1.528"], ["TST", "<1e-07", "0.497", "CWH43", "0.0006", "0.699"], ["SMPDL3A", "1E-07", "0.428", "DHRS11", "0.000607", "0.748"], ["HSD17B11", "1E-07", "2.087", "UGP2", "0.000701", "1.977"], ["ETFDH", "3E-07", "0.549", "SLC22A18AS", "0.000812", "0.558"]], "row_count": 24, "column_count": 6, "numeric_cells": 100, "header_rows": 1, "locator": "section[10]/table-wrap[1]#tI-ol-0-0-7097"}}, {"id": "asset:table:pmid:29344121:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:62e6abdfaa050d25dda06a0016471ac0b6fe89086776477ba108908d8cf4b596", "bytes": 2753, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#tII-ol-0-0-7097", "version": null, "note": "GO analysis and KEGG pathway analysis of 46 survival related-DEGs (partial data).", "structure": {"pmcid": "PMC5754913", "section_index": 11, "section_title": "Validation of DEGs in independent CRC datasets", "row_count": 41, "column_count": 4}, "table": {"label": "Table II.", "caption": "GO analysis and KEGG pathway analysis of 46 survival related-DEGs (partial data).", "rows": [["Genes", "Hyp", "Hypa", "Annotations"], ["Biological process", "", "", ""], ["5", "4.7E-05", "0.00408", "GO:0042493: Response to drug (BP)"], ["4", "0.00079", "0.02956", "GO:0008152: Metabolic process (BP)"], ["3", "0.00804", "0.03142", "GO:0008283: Cell proliferation (BP)"], ["3", "0.00769", "0.03249", "GO:0007411: Axon guidance (BP)"], ["3", "0.01192", "0.0359", "GO:0008284: Positive regulation of cell proliferation (BP)"], ["3", "0.02362", "0.04835", "GO:0045893: Positive regulation of transcription, DNA-dependent (BP)"], ["Molecular function", "", "", ""], ["13", "0.00391", "0.02429", "GO:0005515: Protein binding (MF)"], ["7", "1.6E-06", "0.00019", "GO:0016491: Oxidoreductase activity (MF)"], ["7", "0.01988", "0.04888", "GO:0000166: Nucleotide binding (MF)"], ["6", "0.01607", "0.0431", "GO:0004872: Receptor activity (MF)"], ["5", "0.00871", "0.03213", "GO:0016787: Hydrolase activity (MF)"], ["4", "0.00865", "0.03294", "GO:0016740: Transferase activity (MF)"], ["4", "0.01535", "0.04312", "GO:0004930: G-protein coupled receptor activity (MF)"], ["Cellular component", "", "", ""], ["15", "0.00234", "0.03334", "GO:0005737: Cytoplasm (CC)"], ["13", "0.00169", "0.03219", "GO:0016020: Membrane (CC)"], ["11", "0.00562", "0.03205", "GO:0005886: Plasma membrane (CC)"], ["9", "0.00075", "0.02125", "GO:0005576: Extracellular region (CC)"], ["7", "0.0028", "0.02656", "GO:0005730: Nucleolus (CC)"], ["6", "0.00948", "0.04156", "GO:0005739: Mitochondrion (CC)"], ["5", "0.00357", "0.02911", "GO:0005615: Extracellular space (CC)"], ["4", "0.00072", "0.04092", "GO:0005743: Mitochondrial inner membrane (CC)"], ["3", "0.00236", "0.02696", "GO:0005759: Mitochondrial matrix (CC)"], ["KEGG pathway", "", "", ""], ["3", "0.0089", "0.0411", "(KEGG) 05200: Pathways in cancer"], ["2", "0.00215", "0.02152", "(KEGG) 05213: Endometrial cancer"], ["2", "0.00258", "0.02211", "(KEGG) 05221: Acute myeloid leukemia"], ["2", "0.00304", "0.02282", "(KEGG) 05210: Colorectal cancer"], ["2", "0.00077", "0.02304", "(KEGG) 00040: Pentose and glucuronate interconversions"], ["2", "0.00207", "0.02485", "(KEGG) 00500: Starch and sucrose metabolism"], ["2", "0.00419", "0.02514", "(KEGG) 05220: Chronic myeloid leukemia"], ["2", "0.00386", "0.02574", "(KEGG) 05218: Melanoma"], ["2", "0.00184", "0.02755", "(KEGG) 00520: Amino sugar and nucleotide sugar metabolism"], ["2", "0.00141", "0.02818", "(KEGG) 05219: Bladder cancer"], ["2", "0.00551", "0.03004", "(KEGG) 05222: Small cell lung cancer"], ["2", "0.00063", "0.03755", "(KEGG) 05216: Thyroid cancer"], ["2", "0.01148", "0.04919", "(KEGG) 04110: Cell cycle"], ["2", "0.01238", "0.04953", "(KEGG) 04360: Axon guidance"]], "row_count": 41, "column_count": 4, "numeric_cells": 144, "header_rows": 1, "locator": "section[11]/table-wrap[1]#tII-ol-0-0-7097"}}, {"id": "asset:table:pmid:29344121:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:44629127d9e20636f94c039c2530c96a73961862b4feb3abcd406a700d10eaea", "bytes": 2274, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#tIII-ol-0-0-7097", "version": null, "note": "Multivariable and univariable model tests of risk score and other factors.", "structure": {"pmcid": "PMC5754913", "section_index": 12, "section_title": "Survival analysis of DEGs in CRC and their function annotation", "row_count": 39, "column_count": 9}, "table": {"label": "Table III.", "caption": "Multivariable and univariable model tests of risk score and other factors.", "rows": [["A, GSE14333"], [""], ["", "Multivariable model", "Univariable model"], ["", "", ""], ["Variables", "HR", "95% CI of HR", "", "P-value", "HR", "95% CI of HR", "", "P-value"], ["Risk score", "2.346", "1.298", "4.241", "0.005", "2.718", "1.523", "4.851", "0.001"], ["Location", "0.965", "0.814", "1.144", "0.683", "0.892", "0.76", "1.047", "0.163"], ["Dukes stage", "1.18", "0.926", "1.503", "0.18", "1.044", "0.86", "1.266", "0.666"], ["Age of diagnosis", "1.008", "0.994", "1.023", "0.257", "1.105", "1.002", "1.028", "0.02"], ["Sex", "0.926", "0.683", "1.255", "0.62", "0.877", "0.651", "1.182", "0.39"], ["Adj XRT", "0.463", "0.218", "0.984", "0.045", "0.433", "0.212", "0.884", "0.021"], ["Adj CTX", "0.867", "0.568", "1.325", "0.51", "0.847", "0.618", "1.16", "0.3"], [""], ["B, GSE17536"], [""], ["", "Multivariable model", "Univariable model"], ["", "", ""], ["Variables", "HR", "95% CI of HR", "", "P-value", "HR", "95% CI of HR", "", "P-value"], [""], ["Risk score", "2.745", "1.204", "6.262", "0.016", "3.283", "1.489", "7.236", "0.003"], ["Age", "1.015", "0.999", "1.031", "0.061", "1.018", "1.003", "1.034", "0.016"], ["Sex", "1.084", "0.747", "1.572", "0.672", "0.953", "0.666", "1.362", "0.79"], ["Ethnicity", "0.967", "0.728", "1.284", "0.817", "0.915", "0.685", "1.221", "0.545"], ["AJCC stage", "1.107", "0.892", "1.373", "0.357", "1.051", "0.861", "1.284", "0.625"], ["Grade", "1.254", "0.828", "1.898", "0.285", "1.375", "0.924", "2.045", "0.116"], [""], ["C, GSE29621"], [""], ["", "Multivariable model", "Univariable model"], ["", "", ""], ["Variables", "HR", "95% CI of HR", "", "P-value", "HR", "95% CI of HR", "", "P-value"], [""], ["Risk score", "9.03", "1.425", "57.223", "0.019", "2.526", "0.481", "13.269", "2.73E-05"], ["Sex", "1.243", "0.513", "3.014", "0.63", "1.508", "0.649", "3.505", "0.34"], ["T stage", "0.449", "0.091", "2.209", "0.325", "1.048", "0.438", "2.509", "0.915"], ["N stage", "1.583", "0.604", "4.143", "0.35", "2.688", "1.526", "4.734", "0.001"], ["M stage", "2.065", "0.368", "11.592", "0.41", "4.934", "2.188", "11.124", "1.19E-04"], ["Histology grade", "0.849", "0.325", "2.219", "0.738", "0.665", "0.284", "1.558", "0.348"], ["AJCC stage", "1.965", "0.518", "7.45", "0.321", "2.708", "1.615", "4.542", "1.59E-04"]], "row_count": 39, "column_count": 9, "numeric_cells": 169, "header_rows": 5, "locator": "section[12]/table-wrap[1]#tIII-ol-0-0-7097"}}, {"id": "asset:table:pmid:29344121:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:acbe6cfa18273110159688377390c8a797584ae8c25cd80186570b947776b790", "bytes": 2753, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[2]#tIV-ol-0-0-7097", "version": null, "note": "GO analysis and KEGG pathway analysis of 46 survival related-DEGs (partial data).", "structure": {"pmcid": "PMC5754913", "section_index": 12, "section_title": "Survival analysis of DEGs in CRC and their function annotation", "row_count": 41, "column_count": 4}, "table": {"label": "Table IV.", "caption": "GO analysis and KEGG pathway analysis of 46 survival related-DEGs (partial data).", "rows": [["Genes", "Hyp", "Hypa", "Annotations"], ["Biological process", "", "", ""], ["5", "4.7E-05", "0.00408", "GO:0042493: Response to drug (BP)"], ["4", "0.00079", "0.02956", "GO:0008152: Metabolic process (BP)"], ["3", "0.00804", "0.03142", "GO:0008283: Cell proliferation (BP)"], ["3", "0.00769", "0.03249", "GO:0007411: Axon guidance (BP)"], ["3", "0.01192", "0.0359", "GO:0008284: Positive regulation of cell proliferation (BP)"], ["3", "0.02362", "0.04835", "GO:0045893: Positive regulation of transcription, DNA-dependent (BP)"], ["Molecular function", "", "", ""], ["13", "0.00391", "0.02429", "GO:0005515: Protein binding (MF)"], ["7", "1.6E-06", "0.00019", "GO:0016491: Oxidoreductase activity (MF)"], ["7", "0.01988", "0.04888", "GO:0000166: Nucleotide binding (MF)"], ["6", "0.01607", "0.0431", "GO:0004872: Receptor activity (MF)"], ["5", "0.00871", "0.03213", "GO:0016787: Hydrolase activity (MF)"], ["4", "0.00865", "0.03294", "GO:0016740: Transferase activity (MF)"], ["4", "0.01535", "0.04312", "GO:0004930: G-protein coupled receptor activity (MF)"], ["Cellular component", "", "", ""], ["15", "0.00234", "0.03334", "GO:0005737: Cytoplasm (CC)"], ["13", "0.00169", "0.03219", "GO:0016020: Membrane (CC)"], ["11", "0.00562", "0.03205", "GO:0005886: Plasma membrane (CC)"], ["9", "0.00075", "0.02125", "GO:0005576: Extracellular region (CC)"], ["7", "0.0028", "0.02656", "GO:0005730: Nucleolus (CC)"], ["6", "0.00948", "0.04156", "GO:0005739: Mitochondrion (CC)"], ["5", "0.00357", "0.02911", "GO:0005615: Extracellular space (CC)"], ["4", "0.00072", "0.04092", "GO:0005743: Mitochondrial inner membrane (CC)"], ["3", "0.00236", "0.02696", "GO:0005759: Mitochondrial matrix (CC)"], ["KEGG pathway", "", "", ""], ["3", "0.0089", "0.0411", "(KEGG) 05200: Pathways in cancer"], ["2", "0.00215", "0.02152", "(KEGG) 05213: Endometrial cancer"], ["2", "0.00258", "0.02211", "(KEGG) 05221: Acute myeloid leukemia"], ["2", "0.00304", "0.02282", "(KEGG) 05210: Colorectal cancer"], ["2", "0.00077", "0.02304", "(KEGG) 00040: Pentose and glucuronate interconversions"], ["2", "0.00207", "0.02485", "(KEGG) 00500: Starch and sucrose metabolism"], ["2", "0.00419", "0.02514", "(KEGG) 05220: Chronic myeloid leukemia"], ["2", "0.00386", "0.02574", "(KEGG) 05218: Melanoma"], ["2", "0.00184", "0.02755", "(KEGG) 00520: Amino sugar and nucleotide sugar metabolism"], ["2", "0.00141", "0.02818", "(KEGG) 05219: Bladder cancer"], ["2", "0.00551", "0.03004", "(KEGG) 05222: Small cell lung cancer"], ["2", "0.00063", "0.03755", "(KEGG) 05216: Thyroid cancer"], ["2", "0.01148", "0.04919", "(KEGG) 04110: Cell cycle"], ["2", "0.01238", "0.04953", "(KEGG) 04360: Axon guidance"]], "row_count": 41, "column_count": 4, "numeric_cells": 144, "header_rows": 1, "locator": "section[12]/table-wrap[2]#tIV-ol-0-0-7097"}}, {"id": "asset:table:pmid:29344121:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:57b61393bbf6e5f872dd7ba0fdf987b57d4615e519de7d664605ec55ebd58d7f", "bytes": 2270, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tV-ol-0-0-7097", "version": null, "note": "Multivariable and univariable model tests of risk score and other factors.", "structure": {"pmcid": "PMC5754913", "section_index": 13, "section_title": "Construction of risk score formula", "row_count": 39, "column_count": 9}, "table": {"label": "Table V.", "caption": "Multivariable and univariable model tests of risk score and other factors.", "rows": [["A, GSE14333"], [""], ["", "Multivariable model", "Univariable model"], ["", "", ""], ["Variables", "HR", "95% CI of HR", "", "P-value", "HR", "95% CI of HR", "", "P-value"], ["Risk score", "2.346", "1.298", "4.241", "0.005", "2.718", "1.523", "4.851", "0.001"], ["Location", "0.965", "0.814", "1.144", "0.683", "0.892", "0.76", "1.047", "0.163"], ["Dukes stage", "1.18", "0.926", "1.503", "0.18", "1.044", "0.86", "1.266", "0.666"], ["Age of diagnosis", "1.008", "0.994", "1.023", "0.257", "1.105", "1.002", "1.028", "0.02"], ["Sex", "0.926", "0.683", "1.255", "0.62", "0.877", "0.651", "1.182", "0.39"], ["Adj XRT", "0.463", "0.218", "0.984", "0.045", "0.433", "0.212", "0.884", "0.021"], ["Adj CTX", "0.867", "0.568", "1.325", "0.51", "0.847", "0.618", "1.16", "0.3"], [""], ["B, GSE17536"], [""], ["", "Multivariable model", "Univariable model"], ["", "", ""], ["Variables", "HR", "95% CI of HR", "", "P-value", "HR", "95% CI of HR", "", "P-value"], [""], ["Risk score", "2.745", "1.204", "6.262", "0.016", "3.283", "1.489", "7.236", "0.003"], ["Age", "1.015", "0.999", "1.031", "0.061", "1.018", "1.003", "1.034", "0.016"], ["Sex", "1.084", "0.747", "1.572", "0.672", "0.953", "0.666", "1.362", "0.79"], ["Ethnicity", "0.967", "0.728", "1.284", "0.817", "0.915", "0.685", "1.221", "0.545"], ["AJCC stage", "1.107", "0.892", "1.373", "0.357", "1.051", "0.861", "1.284", "0.625"], ["grade", "1.254", "0.828", "1.898", "0.285", "1.375", "0.924", "2.045", "0.116"], [""], ["C, GSE29621"], [""], ["", "Multivariable model", "Univariable model"], ["", "", ""], ["Variables", "HR", "95% CI of HR", "", "P-value", "HR", "95% CI of HR", "", "P-value"], [""], ["Risk score", "9.03", "1.425", "57.223", "0.019", "2.526", "0.481", "13.269", "2.73E-05"], ["Sex", "1.243", "0.513", "3.014", "0.63", "1.508", "0.649", "3.505", "0.34"], ["T stage", "0.449", "0.091", "2.209", "0.325", "1.048", "0.438", "2.509", "0.915"], ["N stage", "1.583", "0.604", "4.143", "0.35", "2.688", "1.526", "4.734", "0.001"], ["M stage", "2.065", "0.368", "11.592", "0.41", "4.934", "2.188", "11.124", "1.19E-04"], ["Histology grade", "0.849", "0.325", "2.219", "0.738", "0.665", "0.284", "1.558", "0.348"], ["AJCC stage", "1.965", "0.518", "7.45", "0.321", "2.708", "1.615", "4.542", "1.59E-04"]], "row_count": 39, "column_count": 9, "numeric_cells": 169, "header_rows": 5, "locator": "section[13]/table-wrap[1]#tV-ol-0-0-7097"}}], "gaps": ["asset:data:geo:GSE14333 not downloaded", "asset:data:geo:GSE14333 licence not read", "asset:data:geo:GSE17536 not downloaded", "asset:data:geo:GSE17536 licence not read", "asset:data:geo:GSE29621 not downloaded", "asset:data:geo:GSE29621 licence not read", "asset:data:geo:GSE44076 not downloaded", "asset:data:geo:GSE44076 licence not read", "asset:data:geo:GSE44861 not downloaded", "asset:data:geo:GSE44861 licence not read", "asset:data:geo:GSE9348 not downloaded", "asset:data:geo:GSE9348 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Survival analysis was performed by Kaplan-Meier method and Mantel-Cox log-rank test was used to evaluate the statistical significance of the differences."}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "cox regression"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "Chi-Square"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "chi_square_test", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": []}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE9348", "GSE44076", "GSE44861", "GSE14333", "GSE17536", "GSE29621"], "resolved_accessions": ["GSE9348", "GSE44076", "GSE44861", "GSE14333", "GSE17536", "GSE29621"], "statements": ["Data which were not shown in this article could be archived by contacting the corresponding author."], "basis": "The paper names GSE9348, GSE44076, GSE44861, GSE14333, GSE17536, GSE29621 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:29344121", "data:geo:GSE14333", "asset:table:pmid:29344121:1", "asset:table:pmid:29344121:2", "asset:table:pmid:29344121:3", "asset:table:pmid:29344121:4", "asset:table:pmid:29344121:5"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14333"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:33:27Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 8, "usage": {"prompt_tokens": 68168, "completion_tokens": 5838, "cached_tokens": 17944}}, "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:29344121", "type": "paper", "label": "pmid:29344121"}, {"id": "source:pmid:29344121", "type": "manuscript", "label": "PMID 29344121 full text"}, {"id": "data:geo:GSE14333", "type": "dataset", "label": "GEO GSE14333"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29344121", "type": "paper", "label": "pmid:29344121"}, {"id": "source:pmid:29344121", "type": "manuscript", "label": "PMID 29344121 full text"}, {"id": "data:geo:GSE14333", "type": "dataset", "label": "GEO GSE14333"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29344121", "type": "extraction", "used": ["source:pmid:29344121"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14333", "type": "accession_resolution", "used": ["data:geo:GSE14333"], "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": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:29344121", "parent_hash": "sha256:39611db70fb1dcf3ad5725ae37f482c19dfc119b646dfddbe3de1808822ca2a4", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE14333 licence not read", "asset:data:geo:GSE14333 not downloaded", "asset:data:geo:GSE17536 licence not read", "asset:data:geo:GSE17536 not downloaded", "asset:data:geo:GSE29621 licence not read", "asset:data:geo:GSE29621 not downloaded", "asset:data:geo:GSE44076 licence not read", "asset:data:geo:GSE44076 not downloaded", "asset:data:geo:GSE44861 licence not read", "asset:data:geo:GSE44861 not downloaded", "asset:data:geo:GSE9348 licence not read", "asset:data:geo:GSE9348 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Survival analysis was performed by Kaplan-Meier method and Mantel-Cox log-rank test was used to evaluate the statistical significance of the differences."], "order_basis": "analysis_only", "id": "assay:1"}]}