Gene Expression Signature to Predict Prognosis and Adjuvant Chemosensitivity of Colorectal Cancer Patients.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32494194", "kind": "science-record", "revision": 7, "content_hash": "sha256:8f4e0fa08a26a0c0ef48ae0edd54aae3691a09b72301aba0dc60fc5de7844c05", "created_at": "2026-11-01T15:41:03Z", "updated_at": "2026-11-01T22:01:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene Expression Signature to Predict Prognosis and Adjuvant Chemosensitivity of Colorectal Cancer Patients.", "doi": "10.2147/CMAR.S243490", "pmid": "32494194", "authors": ["Jianxia Li", "Jianwei Zhang", "Huabin Hu", "Yue Cai", "Jiayu Ling", "Zehua Wu", "Yanhong Deng"], "journal": "Cancer management and research", "year": 2020, "abstract": "PURPOSE: Molecular characteristics using gene-expression profiling can undoubtedly improve the prediction of treatment responses, and ultimately, the clinical outcome of cancer patients. We aimed at developing a genetic signature to improve the prediction of chemosensitivity and prognosis of patients with colorectal cancer (CRC).\nPATIENTS AND METHODS: We analyzed microarray data of 32 CRC patients to explore the potential functions and pathways involved in the disease relapse in CRC. Gene expression profiles and clinical follow-up information of GSE39582, GSE17536, and GSE103479 were downloaded from the Gene Expression Omnibus database (GEO) to identify prognostic genes. Eventually, a model of 15-mRNA signature was established, in which its efficacy for predicting chemosensitivity and prognosis was examined.\nRESULTS: Based on the proposed model of 15-mRNA signature, the test series patients could be classified into high-risk or low-risk subgroup with significantly different overall survival (OS) rate (hazard ratio [HR]=1.48, 95% confidence interval [CI]=1.30-1.70, P≤0.001). The prognostic value of this 15-mRNA signature was confirmed in another validation series. Further analysis revealed that the prognostic value of this signature was independent of the TNM stage and can predict adjuvant chemosensitivity of patients with early-stage CRC.\nCONCLUSION: We identified a novel 15-mRNA signature in patients with CRC, which could be clinically helpful in the prognosis evaluation and the process of selection of patients with early-stage CRC for undergoing adjuvant chemotherapy.", "claims": [{"id": "claim-method", "statement": "Gene expression profiles and clinical follow-up information of GSE39582, GSE17536, and GSE103479 were downloaded from the Gene Expression Omnibus database (GEO) to identify prognostic genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32494194", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Gene expression profiles and clinical follow-up information of GSE39582, GSE17536, and GSE103479 were downloaded from the Gene Expression Omnibus database (GEO) to identify prognostic genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The microarray data of 32 patients that supported the findings of this study are available from the corresponding author upon request. Public data can be found online at the GEO database (accession nos. GSE39582, GSE17536, and GSE103479).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32494194", "locator": "sections[18] \"Data Sharing Statement\" paragraph 2", "quote": "The microarray data of 32 patients that supported the findings of this study are available from the corresponding author upon request. Public data can be found online at the GEO database (accession nos. GSE39582, GSE17536, and GSE103479)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "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:32494194"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32494194", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/CMAR.S243490", "sha256": "sha256:4a701f330d9ddc77919cfb2f8b275a938606db145da6ed331382d4de70f85113", "bytes": 36346, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/CMAR.S243490", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7227814", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "Gene expression profiles and clinical follow-up information of GSE39582, GSE17536, and GSE103479 were downloaded from the Gene Expression Omnibus database (GEO) to identify prognostic genes."}}, {"id": "method-2", "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-3", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fold_change": "onders was at least two-fold-change and P-value less than 0"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "Limma"}}], "targets": [], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The microarray data of 32 patients that supported the findings of this study are available from the corresponding author upon request. Public data can be found online at the GEO database (accession nos. GSE39582, GSE17536, and GSE103479)."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:32494194"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:03:30Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 28712, "completion_tokens": 1429, "cached_tokens": 520}}, "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:32494194", "type": "paper", "label": "pmid:32494194"}, {"id": "source:pmid:32494194", "type": "manuscript", "label": "PMID 32494194 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32494194", "type": "paper", "label": "pmid:32494194"}, {"id": "source:pmid:32494194", "type": "manuscript", "label": "PMID 32494194 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32494194", "type": "extraction", "used": ["source:pmid:32494194"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:32494194", "parent_hash": "sha256:975cbe9a7478363f5563c42100640baf49c98c404a4aeefe008e4dde84b5a83e", "fork_of": null, "generation": 6}, "gaps": ["execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["cer (CRC). PATIENTS AND METHODS: We analyzed microarray data of 32 CRC patients to explore the poten", "ions, as described previously.22 Analysis of Microarray Data and Functional Enrichment Analysis Raw", "ings, 15-mRNA signature was validated in two microarray cohorts, GSE17536 and GSE103479, with partic", "ier curves for validation of patients in two microarray cohorts of GSE17536 and GSE103479 (N = 332);"], "order_basis": "paper_text_order:429", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Gene expression profiles and clinical follow-up information of GSE39582, GSE17536, and GSE103479 were downloaded from the Gene Expression Omnibus database (GEO) to identify prognostic genes."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}