Integrated Bioinformatics Analysis for Identifying the Significant Genes as Poor Prognostic Markers in Gastric Adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35726219", "kind": "science-record", "revision": 4, "content_hash": "sha256:4d051a32b8300554f1182cec386e4d6e183c9559ba52524766de5059e832893c", "created_at": "2026-11-01T18:14:44Z", "updated_at": "2026-11-01T22:06:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Bioinformatics Analysis for Identifying the Significant Genes as Poor Prognostic Markers in Gastric Adenocarcinoma.", "doi": "10.1155/2022/9080460", "pmid": "35726219", "authors": ["Yamei Li", "Yan Luo", "Qiang Tian", "Yu Lai", "Lei Xu", "Hailong Yun", "Yang Liang", "Dandan Liao", "Rui Gu", "Liye Liu", "Mu Yuan", "Yijiao Li", "Yufan Li", "Mingze Lu", "Xin Yong", "Hua Zhang"], "journal": "Journal of oncology", "year": 2022, "abstract": "Gastric adenocarcinoma (GAC) is the most common histological type of gastric cancer and imposes a considerable health burden globally. The purpose of this study was to identify significant genes and key pathways participated in the initiation and progression of GAC. Four datasets (GSE13911, GSE19826, GSE54129, and GSE79973) including 171 GAC and 77 normal tissues from Gene Expression Omnibus (GEO) database were collected and analyzed. Through integrated bioinformatics analysis, we obtained 69 commonly differentially expressed genes (DEGs) among the four datasets, including 20 upregulated and 49 downregulated genes. The prime module in protein-protein interaction network of DEGs, including ADAMTS2, COL10A1, COL1A1, COL1A2, COL8A1, BGN, and SPP1, was enriched in protein digestion and absorption, ECM-receptor interaction, focal adhesion, PI3K-Akt signaling pathway, and amoebiasis. Furthermore, expression and survival analysis found that all seven hub genes were highly expressed in GAC tissues and 6 of them (except for SPP1) were able to predict poor prognosis of GAC. Finally, we verified the 6 high-expressed hub genes in GAC tissues via immunohistochemistry, Western blot, and RNA quantification analysis. Altogether, we identified six significantly upregulated DEGs as poor prognostic markers in GAC based on integrated bioinformatical methods, which could be potential molecular markers and therapeutic targets for GAC patients.", "claims": [{"id": "claim-method", "statement": "The GEO2R online tools [18] were used to identify DEGs between the GAC specimen and normal specimen with |log2FC| > 2 and an adjusted P value <0.05 [16–18].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35726219", "locator": "sections[4] \"2.2. DEGs Identification\" paragraph 2", "quote": "The GEO2R online tools [18] were used to identify DEGs between the GAC specimen and normal specimen with |log2FC| > 2 and an adjusted P value <0.05 [16–18]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The dataset supporting our findings is available at the following website: https://www.ncbi.nlm.nih.gov/geo/. All data generated or analyzed during this study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35726219", "locator": "sections[22] \"Data Availability\" paragraph 2", "quote": "The dataset supporting our findings is available at the following website: https://www.ncbi.nlm.nih.gov/geo/. All data generated or analyzed during this study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Results showed that a total of 69 commonly DEGs were identified, including 20 upregulated genes (log2FC ＞ 2) and 49 downregulated genes (log2FC ＜ −2) in GAC tissues (Figures 1(b) and 1(c) and Table 1).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35726219", "locator": "sections[12] \"3.1. Identification of DEGs in Gastric Adenocarcinoma\" paragraph 2", "quote": "Results showed that a total of 69 commonly DEGs were identified, including 20 upregulated genes (log2FC ＞ 2) and 49 downregulated genes (log2FC ＜ −2) in GAC tissues (Figures 1(b) and 1(c) and Table 1)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Results showed that a total of 69 commonly DEGs were identified, including 20 upregulated genes (log2FC ＞ 2) and 49 downregulated genes (log2FC ＜ −2) in GAC tissues (Figures 1(b) and 1(c) and Table 1).", "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:35726219"], "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:GSE13911"], "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:GSE13911"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35726219", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/9080460", "sha256": "sha256:8b64c448ef73f6a184e7bea29f865818c8a2267391b1b34aeaacd9fafd674bef", "bytes": 21412, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/9080460", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9206555", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13911", "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=GSE13911", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13911", "version": null, "note": "The dataset supporting our findings is available at the following website: https://www.ncbi.nlm.nih.gov/geo/. 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