Identification of gastric cancer biomarkers through in-silico analysis of microarray based datasets.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39655267", "kind": "science-record", "revision": 3, "content_hash": "sha256:dfef7c5ade3a0edfb38d2107c7a1b13b098f61692e543d9f52afb84ee238cb3e", "created_at": "2026-11-01T20:29:57Z", "updated_at": "2026-11-01T22:55:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of gastric cancer biomarkers through in-silico analysis of microarray based datasets.", "doi": "10.1016/j.bbrep.2024.101880", "pmid": "39655267", "authors": ["Arbaz Akhtar", "Yasir Hameed", "Samina Ejaz", "Iqra Abdullah"], "journal": "Biochemistry and biophysics reports", "year": 2024, "abstract": "Gastric cancer is among the most prevalent cancers worldwide including in Pakistan. Late diagnosis of gastric cancer leads to reduced survival. The present study aimed to investigate biomarkers for early diagnosis and prognosis of gastric cancer. For this purpose, the ten microarray-based gene expression datasets (GSE54129, GSE79973, GSE161533, GSE103236, GSE33651, GSE19826, GSE118916, GSE112369, GSE13911, and GSE81948) were retrieved from GEO database and analyzed by GEO2R to identify differentially expressed genes. Datasets were arranged in subsets of different dataset combinations to identify common DEGs. The gene ontology and functional pathway enrichment analysis of common DEGs was performed by DAVID tool. Pan-cancer analysis was conducted by UALCAN database. Survival analysis of common DEGs was done by Kaplan-Meier plotter. A total of 71 common DEGs were identified in different combinations of datasets. Among them, only 5 DEGs namely ATP4B, ATP4A, CCKBR, KCNJ15, and KCNJ16 were detected to be common in all the datasets. The GO and pathway analysis represented that the identified DEGs are involved in gastric acid secretion and collecting duct acid secretion pathways. Further expression validation of these five genes using three additional datasets (GSE31811, GSE26899, and GSE26272) confirmed their differential expression in gastric cancer samples. The pan-cancer analysis also revealed aberrant expression of DEGs in various cancers. The survival analysis showed the association of these 5 DEGs with poor survival of gastric cancer patients. To conclude, this study revealed a panel of 5 genes, which can be employed as diagnostic and prognostic biomarkers of gastric cancer patients.", "claims": [{"id": "claim-method", "statement": "Identification of DEGs was performed by GEO2R available at (http://www.ncbi.nlm.nih.gov/geo/geo2r).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39655267", "locator": "sections[4] \"Screening for differentially expressed genes (DEGs)\" paragraph 2", "quote": "Identification of DEGs was performed by GEO2R available at (http://www.ncbi.nlm.nih.gov/geo/geo2r)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The analyzed GEO datasets GSE54129, GSE79973, GSE161533, GSE103236, GSE33651, GSE19826, GSE118916, GSE112369, GSE13911, and GSE81948 are available at (https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39655267", "locator": "sections[22] \"Data availability\" paragraph 2", "quote": "The analyzed GEO datasets GSE54129, GSE79973, GSE161533, GSE103236, GSE33651, GSE19826, GSE118916, GSE112369, GSE13911, and GSE81948 are available at (https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified a five-gene panel—ATP4B, ATP4A, CCKBR, KCNJ15, and KCNJ16—as promising diagnostic and prognostic biomarkers for gastric cancer patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39655267", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "To conclude, this study revealed a panel of 5 genes, which can be employed as diagnostic and prognostic biomarkers of gastric cancer patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified a five-gene panel—ATP4B, ATP4A, CCKBR, KCNJ15, and KCNJ16—as promising diagnostic and prognostic biomarkers for gastric cancer 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:39655267"], "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. 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