A transcriptional co-expression network-based approach to identify prognostic biomarkers in gastric carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32095347", "kind": "science-record", "revision": 6, "content_hash": "sha256:b41235cef57c3765f6e836428c857500ad91ae6b6ce3632459d42dcdbfd932a9", "created_at": "2026-11-01T15:40:56Z", "updated_at": "2026-11-01T21:22:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A transcriptional co-expression network-based approach to identify prognostic biomarkers in gastric carcinoma.", "doi": "10.7717/peerj.8504", "pmid": "32095347", "authors": ["Danqi Liu", "Boting Zhou", "Rangru Liu"], "journal": "PeerJ", "year": 2020, "abstract": "BACKGROUND: Gastric carcinoma is a very diverse disease. The progression of gastric carcinoma is influenced by complicated gene networks. This study aims to investigate the actual and potential prognostic biomarkers related to survival in gastric carcinoma patients to further our understanding of tumor biology.\nMETHODS: A weighted gene co-expression network analysis was performed with a transcriptome dataset to identify networks and hub genes relevant to gastric carcinoma prognosis. Data was obtained from 300 primary gastric carcinomas (GSE62254). A validation dataset (GSE34942 and GSE15459) and TCGA dataset confirmed the results. Gene ontology, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and gene set enrichment analysis (GSEA) were performed to identify the clusters responsible for the biological processes and pathways of this disease.\nRESULTS: A brown transcriptional module enriched in the organizational process of the extracellular matrix was significantly correlated with overall survival (HR = 1.586, p = 0.005, 95% CI [1.149-2.189]) and disease-free survival (HR = 1.544, p = 0.008, 95% CI [1.119-2.131]). These observations were confirmed in the validation dataset (HR = 1.664, p = 0.006, 95% CI [1.155-2.398] in overall survival). Ten hub genes were identified and confirmed in the validation dataset from this brown module; five key biomarkers (COL8A1, FRMD6, TIMP2, CNRIP1 and GPR124 (ADGRA2)) were identified for further research in microsatellite instability (MSI) and epithelial-tomesenchymal transition (MSS/EMT) gastric carcinoma molecular subtypes. A high expression of these genes indicated a poor prognosis.\nCONCLUSION: A transcriptional co-expression network-based approach was used to identify prognostic biomarkers in gastric carcinoma. This method may have potential for use in personalized therapies, however, large-scale randomized controlled clinical trials and replication experiments are needed before these key biomarkers can be applied clinically.", "claims": [{"id": "claim-method", "statement": "The relationship between OS/DFS and modules was assessed as a whole using Cox regression analysis with HRs and corresponding p-values (Table 2).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32095347", "locator": "sections[12] \"Gene modules significantly correlated with survival\" paragraph 2", "quote": "The relationship between OS/DFS and modules was assessed as a whole using Cox regression analysis with HRs and corresponding p-values (Table 2)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data is available at:1. NCBI GEO: GSE62254, GSE34942, GSE15459.2. The Cancer Genome Atlas Project database (https://cancergenome.nih.gov/)—TCGA-STAD: TCGA Hub-TCGA Stomach Cancer (STAD)-gene expression RNAseq.3. cBio Cancer Genomics portal: Query-Esophagus/Stomach-Stomach Adenocarcinoma (TCGA, Firehose Legacy)-COL8A1 FRMD6 TIMP2 CNRIP1 ADGRA2.4. Oncomine (https://www.oncomine.org/resource/login.html): -Analysis Type: Gastric Cancer vs. Normal Analysis-COL8A1; Analysis Type: Gastric Cancer vs. Normal Analysis-FRMD6; Analysis Type: Gastric Cancer vs. Normal Analysis-TIMP2; Analysis Type: Gastric Cancer vs. Normal Analysis-CNRIP1; Analysis Type: Gastric Cancer vs. Normal Analysis-GPR124.5. The Human Protein Atlas database (https://www.proteinatlas.org/): COL8A1-Tissue-Pathology; FRMD6-Tissue-Pathology; TIMP2-Tissue- Pathology; GPR124-Tissue-Pathology.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32095347", "locator": "sections[22] \"Additional Information and Declarations\" paragraph 4", "quote": "Data is available at:1. NCBI GEO: GSE62254, GSE34942, GSE15459.2. The Cancer Genome Atlas Project database (https://cancergenome.nih.gov/)—TCGA-STAD: TCGA Hub-TCGA Stomach Cancer (STAD)-gene expression RNAseq.3. cBio Cancer Genomics portal: Query-Esophagus/Stomach-Stomach Adenocarcinoma (TCGA, Firehose Legacy)-COL8A1 FRMD6 TIMP2 CNRIP1 ADGRA2.4. Oncomine (https://www.oncomine.org/resource/login.html): -Analysis Type: Gastric Cancer vs. Normal Analysis-COL8A1; Analysis Type: Gastric Cancer vs. Normal Analysis-FRMD6; Analysis Type: Gastric Cancer vs. Normal Analysis-TIMP2; Analysis Type: Gastric Cancer vs. Normal Analysis-CNRIP1; Analysis Type: Gastric Cancer vs. Normal Analysis-GPR124.5. The Human Protein Atlas database (https://www.proteinatlas.org/): COL8A1-Tissue-Pathology; FRMD6-Tissue-Pathology; TIMP2-Tissue- Pathology; GPR124-Tissue-Pathology."}], "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:32095347"], "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:GSE15459"], "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:GSE15459"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32095347", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.8504", "sha256": "sha256:8b40296f7e4907d62e04622a00d0fbc729a14f2c990be059b599e0b0faee32a2", "bytes": 39039, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.8504", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7025707", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE15459", "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=GSE15459", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15459", "version": null, "note": "Data is available at:1. NCBI GEO: GSE62254, GSE34942, GSE15459.2. The Cancer Genome Atlas Project database (https://cancergenome.nih.gov/)—TCGA-STAD: TCGA Hub-TCGA Stomach Cancer (STAD)-gene expression RNAseq.3. cBio Cancer Genomics portal: Query-Esophagus/Stomach-Stomach Adenocarcinoma (TCGA, Firehose Legacy)-COL8A1 FRMD6 TIMP2 CNRIP1 ADGRA2.4. Oncomine (https://www.oncomine.org/resource/login.html): -Analysis Type: Gastric Cancer vs. Normal Analysis-COL8A1; Analysis Type: Gastric Cancer vs. Normal Analysis-FRMD6; Analysis Type: Gastric Cancer vs. Normal Analysis-TIMP2; Analysis Type: Gastric Cancer vs. Normal Analysis-CNRIP1; Analysis Type: Gastric Cancer vs. Normal Analysis-GPR124.5. The Human Protein Atlas database (https://www.proteinatlas.org/): COL8A1-Tissue-Pathology; FRMD6-Tissue-Pathology; TIMP2-Tissue- Pathology; GPR124-Tissue-Pathology.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data is available at:1. NCBI GEO: GSE62254, GSE34942, GSE15459.2. The Cancer Genome Atlas Project database (https://cancergenome.nih.gov/)—TCGA-STAD: TCGA Hub-TCGA Stomach Cancer (STAD)-gene expression RNAseq.3. cBio Cancer Genomics portal: Query-Esophagus/Stomach-Stomach Adenocarcinoma (TCGA, Firehose Legacy)-COL8A1 FRMD6 TIMP2 CNRIP1 ADGRA2.4. Oncomine (https://www.oncomine.org/resource/login.html): -Analysis Type: Gastric Cancer vs. Normal Analysis-COL8A1; Analysis Type: Gastric Cancer vs. Normal Analysis-FRMD6; Analysis Type: Gastric Cancer vs. Normal Analysis-TIMP2; Analysis Type: Gastric Cancer vs. Normal Analysis-CNRIP1; Analysis Type: Gastric Cancer vs. Normal Analysis-GPR124.5. 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NCBI GEO: GSE62254, GSE34942, GSE15459.2. The Cancer Genome Atlas Project database (https://cancergenome.nih.gov/)—TCGA-STAD: TCGA Hub-TCGA Stomach Cancer (STAD)-gene expression RNAseq.3. cBio Cancer Genomics portal: Query-Esophagus/Stomach-Stomach Adenocarcinoma (TCGA, Firehose Legacy)-COL8A1 FRMD6 TIMP2 CNRIP1 ADGRA2.4. Oncomine (https://www.oncomine.org/resource/login.html): -Analysis Type: Gastric Cancer vs. Normal Analysis-COL8A1; Analysis Type: Gastric Cancer vs. Normal Analysis-FRMD6; Analysis Type: Gastric Cancer vs. Normal Analysis-TIMP2; Analysis Type: Gastric Cancer vs. Normal Analysis-CNRIP1; Analysis Type: Gastric Cancer vs. Normal Analysis-GPR124.5. The Human Protein Atlas database (https://www.proteinatlas.org/): COL8A1-Tissue-Pathology; FRMD6-Tissue-Pathology; TIMP2-Tissue- Pathology; GPR124-Tissue-Pathology.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data is available at:1. NCBI GEO: GSE62254, GSE34942, GSE15459.2. The Cancer Genome Atlas Project database (https://cancergenome.nih.gov/)—TCGA-STAD: TCGA Hub-TCGA Stomach Cancer (STAD)-gene expression RNAseq.3. cBio Cancer Genomics portal: Query-Esophagus/Stomach-Stomach Adenocarcinoma (TCGA, Firehose Legacy)-COL8A1 FRMD6 TIMP2 CNRIP1 ADGRA2.4. Oncomine (https://www.oncomine.org/resource/login.html): -Analysis Type: Gastric Cancer vs. Normal Analysis-COL8A1; Analysis Type: Gastric Cancer vs. Normal Analysis-FRMD6; Analysis Type: Gastric Cancer vs. Normal Analysis-TIMP2; Analysis Type: Gastric Cancer vs. Normal Analysis-CNRIP1; Analysis Type: Gastric Cancer vs. Normal Analysis-GPR124.5. The Human Protein Atlas database (https://www.proteinatlas.org/): COL8A1-Tissue-Pathology; FRMD6-Tissue-Pathology; TIMP2-Tissue- Pathology; GPR124-Tissue-Pathology.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM858082", "GSM858083", "GSM858084", "GSM858085", "GSM858086", "GSM858087", "GSM858088", "GSM858089", "GSM858090", "GSM858091", "GSM858092", "GSM858093", "GSM858094", "GSM858095", "GSM858096", "GSM858097", "GSM858098", "GSM858099", "GSM858100", "GSM858101", "GSM858102", "GSM858103", "GSM858104", "GSM858105", "GSM858106", "GSM858107", "GSM858108", "GSM858109", "GSM858110", "GSM858111", "GSM858112", "GSM858113", "GSM858114", "GSM858115", "GSM858116", "GSM858117", "GSM858118", "GSM858119", "GSM858120", "GSM858121", "GSM858122", "GSM858123", "GSM858124", "GSM858125", "GSM858126", "GSM858127", "GSM858128", "GSM858129", "GSM858130", "GSM858131", "GSM858132", "GSM858133", "GSM858134", "GSM858135", "GSM858136", "GSM858137"], "sample_count": 56, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gastric cancer subtyping (Singapore Patient Cohort, batch B)", "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:GSE62254", "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=GSE62254", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62254", "version": null, "note": "Data is available at:1. NCBI GEO: GSE62254, GSE34942, GSE15459.2. The Cancer Genome Atlas Project database (https://cancergenome.nih.gov/)—TCGA-STAD: TCGA Hub-TCGA Stomach Cancer (STAD)-gene expression RNAseq.3. cBio Cancer Genomics portal: Query-Esophagus/Stomach-Stomach Adenocarcinoma (TCGA, Firehose Legacy)-COL8A1 FRMD6 TIMP2 CNRIP1 ADGRA2.4. Oncomine (https://www.oncomine.org/resource/login.html): -Analysis Type: Gastric Cancer vs. Normal Analysis-COL8A1; Analysis Type: Gastric Cancer vs. Normal Analysis-FRMD6; Analysis Type: Gastric Cancer vs. Normal Analysis-TIMP2; Analysis Type: Gastric Cancer vs. Normal Analysis-CNRIP1; Analysis Type: Gastric Cancer vs. Normal Analysis-GPR124.5. The Human Protein Atlas database (https://www.proteinatlas.org/): COL8A1-Tissue-Pathology; FRMD6-Tissue-Pathology; TIMP2-Tissue- Pathology; GPR124-Tissue-Pathology.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data is available at:1. NCBI GEO: GSE62254, GSE34942, GSE15459.2. The Cancer Genome Atlas Project database (https://cancergenome.nih.gov/)—TCGA-STAD: TCGA Hub-TCGA Stomach Cancer (STAD)-gene expression RNAseq.3. cBio Cancer Genomics portal: Query-Esophagus/Stomach-Stomach Adenocarcinoma (TCGA, Firehose Legacy)-COL8A1 FRMD6 TIMP2 CNRIP1 ADGRA2.4. Oncomine (https://www.oncomine.org/resource/login.html): -Analysis Type: Gastric Cancer vs. Normal Analysis-COL8A1; Analysis Type: Gastric Cancer vs. Normal Analysis-FRMD6; Analysis Type: Gastric Cancer vs. Normal Analysis-TIMP2; Analysis Type: Gastric Cancer vs. Normal Analysis-CNRIP1; Analysis Type: Gastric Cancer vs. Normal Analysis-GPR124.5. 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