Identification of hub genes and construction of an mRNA-miRNA-lncRNA network of gastric carcinoma using integrated bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34968391", "kind": "science-record", "revision": 4, "content_hash": "sha256:432b31779d503eebbeb3aa29d2ca3bd976d013c0fa2ad235b4a17ff11e73c514", "created_at": "2026-11-01T17:36:40Z", "updated_at": "2026-11-01T22:05:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of hub genes and construction of an mRNA-miRNA-lncRNA network of gastric carcinoma using integrated bioinformatics analysis.", "doi": "10.1371/journal.pone.0261728", "pmid": "34968391", "authors": ["Gang Wei", "Youhong Dong", "Zhongshi He", "Hu Qiu", "Yong Wu", "Yongshun Chen"], "journal": "PloS one", "year": 2021, "abstract": "BACKGROUND: Gastric carcinoma (GC) is one of the most common cancer globally. Despite its worldwide decline in incidence and mortality over the past decades, gastric cancer still has a poor prognosis. However, the key regulators driving this process and their exact mechanisms have not been thoroughly studied. This study aimed to identify hub genes to improve the prognostic prediction of GC and construct a messenger RNA-microRNA-long non-coding RNA(mRNA-miRNA-lncRNA) regulatory network.\nMETHODS: The GSE66229 dataset, from the Gene Expression Omnibus (GEO) database, and The Cancer Genome Atlas (TCGA) database were used for the bioinformatic analysis. Differential gene expression analysis methods and Weighted Gene Co-expression Network Analysis (WGCNA) were used to identify a common set of differentially co-expressed genes in GC. The genes were validated using samples from TCGA database and further validation using the online tools GEPIA database and Kaplan-Meier(KM) plotter database. Gene set enrichment analysis(GSEA) was used to identify hub genes related to signaling pathways in GC. The RNAInter database and Cytoscape software were used to construct an mRNA-miRNA-lncRNA network.\nRESULTS: A total of 12 genes were identified as the common set of differentially co-expressed genes in GC. After verification of these genes, 3 hub genes, namely CTHRC1, FNDC1, and INHBA, were found to be upregulated in tumor and associated with poor GC patient survival. In addition, an mRNA-miRNA-lncRNA regulatory network was established, which included 12 lncRNAs, 5 miRNAs, and the 3 hub genes.\nCONCLUSIONS: In summary, the identification of these hub genes and the establishment of the mRNA-miRNA-lncRNA regulatory network provide new insights into the underlying mechanisms of gastric carcinogenesis. In addition, the identified hub genes, CTHRC1, FNDC1, and INHBA, may serve as novel prognostic biomarkers and therapeutic targets.", "claims": [{"id": "claim-method", "statement": "Differential gene expression analysis methods and Weighted Gene Co-expression Network Analysis (WGCNA) were used to identify a common set of differentially co-expressed genes in GC.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34968391", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Differential gene expression analysis methods and Weighted Gene Co-expression Network Analysis (WGCNA) were used to identify a common set of differentially co-expressed genes in GC."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression profiles in dataset GSE66229, which consists of the GSE62254 and GSE66222 datasets, obtained on the GPL570 platform using the Affymetrix Human Genome U133 Plus 2.0 array, (Affymetrix Inc., Santa Clara, CA, USA), were downloaded from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/gds). The GSE66222 dataset contains data from 100 samples of normal gastric tissue, and the GSE62254 dataset contains data from 300 gastric cancer samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34968391", "locator": "sections[3] \"Data sources and pre-processing\" paragraph 2", "quote": "The gene expression profiles in dataset GSE66229, which consists of the GSE62254 and GSE66222 datasets, obtained on the GPL570 platform using the Affymetrix Human Genome U133 Plus 2.0 array, (Affymetrix Inc., Santa Clara, CA, USA), were downloaded from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/gds). The GSE66222 dataset contains data from 100 samples of normal gastric tissue, and the GSE62254 dataset contains data from 300 gastric cancer samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Three hub genes, CTHRC1, FNDC1, and INHBA, were identified as upregulated in gastric carcinoma and associated with poor patient survival.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34968391", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "After verification of these genes, 3 hub genes, namely CTHRC1, FNDC1, and INHBA, were found to be upregulated in tumor and associated with poor GC patient survival."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Three hub genes, CTHRC1, FNDC1, and INHBA, were identified as upregulated in gastric carcinoma and associated with poor patient survival.", "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:34968391"], "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:GSE66229"], "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:GSE66229"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34968391", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1371/journal.pone.0261728", "sha256": "sha256:6659b93b19e287c306b58c90beb1bef593424380213289c8c4a4983cb37645b7", "bytes": 25635, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1371/journal.pone.0261728", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8718005", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE66229", "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=GSE66229", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE66229", "version": null, "note": "The gene expression profiles in dataset GSE66229, which consists of the GSE62254 and GSE66222 datasets, obtained on the GPL570 platform using the Affymetrix Human Genome U133 Plus 2.0 array, (Affymetrix Inc., Santa Clara, CA, USA), were downloaded from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/gds). 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