Identification of G6PC as a potential prognostic biomarker in hepatocellular carcinoma based on bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35984176", "kind": "science-record", "revision": 4, "content_hash": "sha256:f27fac07f8e79c11ae32173b8a454a10a6f4aa3867eba9171f371bed6de39aff", "created_at": "2026-11-01T18:15:07Z", "updated_at": "2026-11-01T22:07:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of G6PC as a potential prognostic biomarker in hepatocellular carcinoma based on bioinformatics analysis.", "doi": "10.1097/MD.0000000000029548", "pmid": "35984176", "authors": ["Li Tian", "Yong Liao"], "journal": "Medicine", "year": 2022, "abstract": "Hepatocellular carcinoma (HCC) has high mortality and incidence rates around the world with limited therapeutic options. There is an urgent need for identification of novel therapeutic targets and biomarkers for early diagnosis and predicting patient survival with HCC. Several studies (GSE102083, GSE29722, GSE101685, and GSE112790) from the GEO database in HCC were screened and analyzed by GEO2R, gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were conducted with the Database for Annotation, Visualization and Integrated Discovery. The protein-protein interaction network was plotted and the module analysis was performed using Search Tool for the Retrieval of Inter-acting Genes/Proteins database and Cytoscape. The expression and survival of key genes were identified using UALCAN, Kaplan-Meier Plotter and ONCOMINE online databases, and the immune infiltration level of key genes was analyzed via the Tumor Immune Estimation Resource (TIMER) database. Through database analysis, eight key genes were finally screened out, and the expressions of cyclin-dependent kinase regulatory subunit 2 and glucose-6-phosphatase catalytic (G6PC), which were closely related to the survival of HCC patients, was detected by using UALCAN. Further analysis on the differential expression of G6PC in multiple cancerous tumors and normal tissues revealed low expression in many solid tumors by Oncomine and TIMER. In addition, Kaplan-Meier plotter and UALCAN database analysis to access diseases prognosis suggested that low expression of G6PC was significantly associated with poor overall survival in HCC patients. Finally, TIMER database analysis showed a significant negative correlation between G6PC and infiltration levels of six kinds of immune cells. The somatic copy number alterations of G6PC were associated with B cells, CD8+ T cells, CD4+ T cells, macrophages, dentritic cells and neutrophils. These bioinformatic data identified G6PC as a potential key gene in the diagnosis and prognosis of HCC.", "claims": [{"id": "claim-method", "statement": "GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/)[21] can help us to analyze DEGs, which is an useful online software. Setting adjusted P < .05 and LogFC (Fold Change) > 1.5 or <−1.5 to define DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35984176", "locator": "sections[4] \"2.2. Identification of DEGs\" paragraph 2", "quote": "GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/)[21] can help us to analyze DEGs, which is an useful online software. Setting adjusted P < .05 and LogFC (Fold Change) > 1.5 or <−1.5 to define DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data sharing not applicable to this article as no datasets were generated or analyzed during the current study.The datasets generated during and/or analyzed during the current study are publicly available. Gene Expression Omnibus: https://www.ncbi.nlm.nih.gov/geo/", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35984176", "locator": "sections[19] \"fn-group\" paragraph 1", "quote": "Data sharing not applicable to this article as no datasets were generated or analyzed during the current study.The datasets generated during and/or analyzed during the current study are publicly available. Gene Expression Omnibus: https://www.ncbi.nlm.nih.gov/geo/"}], "state": "complete"}, {"id": "claim-target-result", "statement": "GEO2R analysis of four GEO microarray datasets yielded 337 common differentially expressed genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35984176", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Several studies (GSE102083, GSE29722, GSE101685, and GSE112790) from the GEO database in HCC were screened and analyzed by GEO2R, gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were conducted with the Database for Annotation, Visualization and Integrated Discovery."}, {"asset": "source:pmid:35984176", "locator": "sections[10] \"3.1. Screening and identification of DEGs in HCC\" paragraph 2", "quote": "A sum of 337 common DEGs (Fig. 1A) was found in all four datasets, consisting of 126 upregulated genes (Fig. 1B) and 211 down-regulated genes (Fig. 1C)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "GEO2R analysis of four GEO microarray datasets yielded 337 common differentially expressed genes.", "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:35984176"], "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:GSE101685"], "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:GSE101685"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35984176", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/MD.0000000000029548", "sha256": "sha256:99d4612e4491c7b684c308b87bcc9733db346b6b1bb698daea3b90bd2f529532", "bytes": 30762, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/MD.0000000000029548", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9388022", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE101685", "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=GSE101685", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE101685", "version": null, "note": "Data sharing not applicable to this article as no datasets were generated or analyzed during the current study.The datasets generated during and/or analyzed during the current study are publicly available. 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