Identification of glioblastoma gene prognosis modules based on weighted gene co-expression network analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30382873", "kind": "science-record", "revision": 6, "content_hash": "sha256:2db6a2ece60bb389af1b3782f5dd0a3cc868d1fc187c83b1a49007b6fa3dc563", "created_at": "2026-11-01T15:40:38Z", "updated_at": "2026-11-01T21:21:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of glioblastoma gene prognosis modules based on weighted gene co-expression network analysis.", "doi": "10.1186/s12920-018-0407-1", "pmid": "30382873", "authors": ["Pengfei Xu", "Jian Yang", "Junhui Liu", "Xue Yang", "Jianming Liao", "Fanen Yuan", "Yang Xu", "Baohui Liu", "Qianxue Chen"], "journal": "BMC medical genomics", "year": 2018, "abstract": "BACKGROUND: Glioblastoma multiforme, the most prevalent and aggressive brain tumour, has a poor prognosis. The molecular mechanisms underlying gliomagenesis remain poorly understood. Therefore, molecular research, including various markers, is necessary to understand the occurrence and development of glioma.\nMETHOD: Weighted gene co-expression network analysis (WGCNA) was performed to construct a gene co-expression network in TCGA glioblastoma samples. Gene ontology (GO) and pathway-enrichment analysis were used to identify significance of gene modules. Cox proportional hazards regression model was used to predict outcome of glioblastoma patients.\nRESULTS: We performed weighted gene co-expression network analysis (WGCNA) and identified a gene module (yellow module) related to the survival time of TCGA glioblastoma samples. Then, 228 hub genes were calculated based on gene significance (GS) and module significance (MS). Four genes (OSMR + SOX21 + MED10 + PTPRN) were selected to construct a Cox proportional hazards regression model with high accuracy (AUC = 0.905). The prognostic value of the Cox proportional hazards regression model was also confirmed in GSE16011 dataset (GBM: n = 156).\nCONCLUSION: We developed a promising mRNA signature for estimating overall survival in glioblastoma patients.", "claims": [{"id": "claim-method", "statement": "WGCNA was performed using the R package WGCNA [10].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30382873", "locator": "sections[4] \"Weighted gene co-expression network analysis and module preservation\" paragraph 2", "quote": "WGCNA was performed using the R package WGCNA [10]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The RNA sequencing data of human glioblastoma samples were obtained from the TCGA data portal (https://portal.gdc.cancer.gov). GeneChip data were retrieved from the GEO data repository (http://www.ncbi.nlm.nih.gov/geo/) with the accession numbers GSE36245, GSE16011 and GSE50161. GlioVis database can be accessed with the http: //gliovis.bioinfo.cnio.es.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30382873", "locator": "sections[25] \"Availability of data and materials\" paragraph 2", "quote": "The RNA sequencing data of human glioblastoma samples were obtained from the TCGA data portal (https://portal.gdc.cancer.gov). GeneChip data were retrieved from the GEO data repository (http://www.ncbi.nlm.nih.gov/geo/) with the accession numbers GSE36245, GSE16011 and GSE50161. GlioVis database can be accessed with the http: //gliovis.bioinfo.cnio.es."}], "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:30382873"], "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:GSE16011"], "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:GSE16011"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30382873", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12920-018-0407-1", "sha256": "sha256:e34f796cf357eab65991cca7ca8830611e4276ec1c901bf55935bbaab0eaa30d", "bytes": 37161, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12920-018-0407-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6211550", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE16011", "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=GSE16011", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16011", "version": null, "note": "The RNA sequencing data of human glioblastoma samples were obtained from the TCGA data portal (https://portal.gdc.cancer.gov). GeneChip data were retrieved from the GEO data repository (http://www.ncbi.nlm.nih.gov/geo/) with the accession numbers GSE36245, GSE16011 and GSE50161. GlioVis database can be accessed with the http: //gliovis.bioinfo.cnio.es.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The RNA sequencing data of human glioblastoma samples were obtained from the TCGA data portal (https://portal.gdc.cancer.gov). GeneChip data were retrieved from the GEO data repository (http://www.ncbi.nlm.nih.gov/geo/) with the accession numbers GSE36245, GSE16011 and GSE50161. 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