Identification of candidate biomarkers associated with gastric cancer prognosis based on an integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36092336", "kind": "science-record", "revision": 5, "content_hash": "sha256:baea52bd9f7ba7db9d12eff3edd5cb90fd670281c7017454de68a73009679a63", "created_at": "2026-11-01T18:15:19Z", "updated_at": "2026-11-01T22:50:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of candidate biomarkers associated with gastric cancer prognosis based on an integrated bioinformatics analysis.", "doi": "10.21037/jgo-22-651", "pmid": "36092336", "authors": ["Yong Liu", "Da-Xiu Wang", "Xiao-Jing Wan", "Xian-Hong Meng"], "journal": "Journal of gastrointestinal oncology", "year": 2022, "abstract": "Background: This study sought to identify candidate biomarkers associated with gastric cancer (GC) prognosis based on an integrated bioinformatics analysis.\nMethods: First, the GSE54129 and GSE79973 data sets were downloaded from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) identified between the 2 data sets were screened using the limma software package in R, and the intersection DEGs were obtained by a Venn analysis. Subsequently, gene clustering and a functional analysis were performed to explore the roles of the DEGs. The protein-protein interaction (PPI) network of the genes in clusters was constructed using the Search Tool for the Retrieval of Interacting Genes/Proteins. A survival analysis evaluated the associations between the candidate genes and the overall survival of GC patients. A drug-gene interaction analysis and an external data set analysis were conducted using The Cancer Genome Atlas-Stomach Adenocarcinoma (TCGA-STAD) data set to validate the prognostic genes.\nResults: We extracted 421 intersection DEGs from the 2 GEO data sets. There were 5 gene clusters, and the functional analysis revealed that they were mainly associated with the extracellular matrix-receptor interaction pathway. The PPI interaction analysis identified the top 36 hub genes. The survival analysis revealed that 7 upregulated genes [i.e., platelet-derived growth factor receptor beta (PDGFRB), angiopoietin 2 (ANGPT2), vascular endothelial growth factor C (VEGFC), collagen type IV alpha 2 chain (COL4A2), collagen type IV alpha 1 chain (COL4A1), thrombospondin 1 (THBS1), and fibronectin 1 (FN1)] were associated with the survival prognosis of GC patients. The 20 drug-gene interaction pairs among the 4 genes and 18 drugs were obtained. Finally, TCGA-STAD data set was used to validate the expression levels of COL4A1, PDGFRB, and FN1.\nConclusions: We found that 7 upregulated genes (i.e., PDGFRB, ANGPT2, VEGFC, COL4A2, COL4A1, THBS1, and FN1) were promising markers of prognosis in GC patients.", "claims": [{"id": "claim-method", "statement": "We used the R limma package (version 3.10.3; http://www.bioconductor.org/packages/2.9/bioc/html/limma.html) to screen for DEGs between the tumor and control samples (11). The P value was calculated and adjusted using the Benjamini-Hochberg method (12).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36092336", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "We used the R limma package (version 3.10.3; http://www.bioconductor.org/packages/2.9/bioc/html/limma.html) to screen for DEGs between the tumor and control samples (11). The P value was calculated and adjusted using the Benjamini-Hochberg method (12)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We obtained the GSE54129 data set (comprising 111 GC and 21 normal control samples) and GSE79973 data set (comprising 10 GC and 10 normal control samples) from the GEO (http://www.ncbi.nlm.nih.gov/geo/) database using the keywords “gastric cancer, Homo sapiens and tissue” based on the GPL570 (HG-U133_Plus_2) Affymetrix Human Genome U133 Plus 2.0 Array.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36092336", "locator": "sections[3] \"Data source and pre-processing\" paragraph 2", "quote": "We obtained the GSE54129 data set (comprising 111 GC and 21 normal control samples) and GSE79973 data set (comprising 10 GC and 10 normal control samples) from the GEO (http://www.ncbi.nlm.nih.gov/geo/) database using the keywords “gastric cancer, Homo sapiens and tissue” based on the GPL570 (HG-U133_Plus_2) Affymetrix Human Genome U133 Plus 2.0 Array."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We found that 7 upregulated genes (i.e., PDGFRB, ANGPT2, VEGFC, COL4A2, COL4A1, THBS1, and FN1) were promising markers of prognosis in GC patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36092336", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "We found that 7 upregulated genes (i.e., PDGFRB, ANGPT2, VEGFC, COL4A2, COL4A1, THBS1, and FN1) were promising markers of prognosis in GC patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We found that 7 upregulated genes (i.e., PDGFRB, ANGPT2, VEGFC, COL4A2, COL4A1, THBS1, and FN1) were promising markers of prognosis in GC patients.", "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:36092336"], "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:GSE54129"], "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:GSE54129"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36092336", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/jgo-22-651", "sha256": 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control samples) from the GEO (http://www.ncbi.nlm.nih.gov/geo/) database using the keywords “gastric cancer, Homo sapiens and tissue” based on the GPL570 (HG-U133_Plus_2) Affymetrix Human Genome U133 Plus 2.0 Array.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We obtained the GSE54129 data set (comprising 111 GC and 21 normal control samples) and GSE79973 data set (comprising 10 GC and 10 normal control samples) from the GEO (http://www.ncbi.nlm.nih.gov/geo/) database using the keywords “gastric cancer, Homo sapiens and tissue” based on the GPL570 (HG-U133_Plus_2) Affymetrix Human Genome U133 Plus 2.0 Array.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1308392", "GSM1308393", "GSM1308394", "GSM1308395", "GSM1308396", "GSM1308397", "GSM1308398", "GSM1308399", "GSM1308400", "GSM1308401", "GSM1308402", "GSM1308403", "GSM1308404", "GSM1308405", "GSM1308406", "GSM1308407", "GSM1308408", 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