Prognostic nomogram of hypoxia-related genes predicting overall survival of colorectal cancer-Analysis of TCGA database.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30755640", "kind": "science-record", "revision": 4, "content_hash": "sha256:f96fe222e6d434c45f84451322d723d096bb2e5c8680c35a7a35a36333893a49", "created_at": "2026-11-01T15:40:42Z", "updated_at": "2026-11-01T21:21:59Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic nomogram of hypoxia-related genes predicting overall survival of colorectal cancer-Analysis of TCGA database.", "doi": "10.1038/s41598-018-38116-y", "pmid": "30755640", "authors": ["Joon-Hyop Lee", "Sohee Jung", "Won Seo Park", "Eun Kyung Choe", "Eunyoung Kim", "Rumi Shin", "Seung Chul Heo", "Jae Hyun Lee", "Kwangsoo Kim", "Young Jun Chai"], "journal": "Scientific reports", "year": 2019, "abstract": "Hypoxia-related gene (HRG) expression is associated with survival outcomes of colorectal cancer (CRC). Our aim was developing a nomogram predicting CRC overall survival (OS) with HRGs and clinicopathological factors. The Cancer Genome Atlas (TCGA) database was used as discovery cohort and two Gene Expression Omnibus databases (GSE39582 and GSE41258) served as validation cohorts. A genetic risk score model prognosticating OS was developed using mRNA expression level of HRGs. Nomogram predicting OS was developed using genetic risk score model and clinicopathological variables. The genetic risk score model included four HRGs (HSPA1L, PUM1, UBE2D2, and HSP27) and successfully prognosticated OS of discovery and two validation cohorts (p < 0.001 for TCGA discovery set, p < 0.003 for the GSE39582 and p = 0.042 for the GSE41258 datasets). Nomogram included genetic risk score, age, and TNM stage. Harrell's concordance indexes of the nomogram were higher than those of TNM stage alone in the discovery set (0.77 vs. 0.69, p < 0.001), GSE39582 (0.65 vs. 0.63, p < 0.001), and GSE41258 datasets (0.78 vs. 0.77, p < 0.001). Our nomogram successfully predicted OS of CRC patients. The mRNA expression level of the HRGs might be useful as an ancillary marker for prognosticating CRC outcome.", "claims": [{"id": "claim-method", "statement": "To evaluate the prognostic value of the genetic risk score in the context of other clinical variables, univariate and multivariate Cox analyses for OS were performed, including the genetic risk score and the conventional clinicopathologic variables (age, gender, TNM stage, KRAS mutation, BRAF mutation, and microsatellite instability).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30755640", "locator": "sections[12] \"Incorporating clinical factors to predict cancer survival\" paragraph 2", "quote": "To evaluate the prognostic value of the genetic risk score in the context of other clinical variables, univariate and multivariate Cox analyses for OS were performed, including the genetic risk score and the conventional clinicopathologic variables (age, gender, TNM stage, KRAS mutation, BRAF mutation, and microsatellite instability)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available from the Cancer Genome Atlas (TCGA, http://cancergenome.nih.gov/) COADREAD project and Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/), accession number GSE39582 and GSE41258.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30755640", "locator": "sections[16] \"Data Availability\" paragraph 2", "quote": "The data that support the findings of this study are available from the Cancer Genome Atlas (TCGA, http://cancergenome.nih.gov/) COADREAD project and Gene Expression Omnibus (GEO, https://www.ncbi.nlm.nih.gov/geo/), accession number GSE39582 and GSE41258."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:30755640"], "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:GSE39582"], "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:GSE39582"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30755640", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-018-38116-y", "sha256": "sha256:135fcc697f7895fc24f849371a5bcbcb1335ba364079d9a9945817412889ee10", "bytes": 29929, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-018-38116-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6372658", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE39582", "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=GSE39582", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39582", "version": null, "note": "The data that support the findings of this study are available from the Cancer Genome Atlas (TCGA, http://cancergenome.nih.gov/) 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