A new finding in the key prognosis-related proto-oncogene FYN in hepatocellular carcinoma based on the WGCNA hub-gene screening trategy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35397600", "kind": "science-record", "revision": 4, "content_hash": "sha256:0b190d1aaaa20b1cee6d2cb2c3eb34e90ba131103f942849d5c9bcc275fa2254", "created_at": "2026-11-01T18:14:13Z", "updated_at": "2026-11-01T22:06:16Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A new finding in the key prognosis-related proto-oncogene FYN in hepatocellular carcinoma based on the WGCNA hub-gene screening trategy.", "doi": "10.1186/s12885-022-09388-5", "pmid": "35397600", "authors": ["Chenkai Huang", "Juanjuan Zhou", "Yuan Nie", "Guihai Guo", "Anjiang Wang", "Xuan Zhu"], "journal": "BMC cancer", "year": 2022, "abstract": "BACKGROUND: Hepatocellular carcinoma (HCC) is the third-most deadly cancer worldwide. More breakthroughs are needed in the clinical practice for liver cancer are needed, and new treatment strategies are required. This study aims to determine the significant differences in genes associated with LIHC and further analyze its prognostic value further.\nMETHODS: Here, we used the TCGA-LIHC database and the profiles of GSE25097 from GEO to explore the differentially co-expressed genes in HCC tissues compared with paratumor (or healthy) tissues. Then, we utilized WGCNA to screen differentially co-expressed genes. Finally, we explored the function of FYN in HCC cells and xenograft tumor models.\nRESULTS: We identified ten hub genes in the protein-protein interaction (PPI) network, but only three (COLEC10, TGFBR3, and FYN) appeared closely related to the prognosis. The expression of FYN was positively correlated with the prognosis of HCC patients. The xenograft model showed that overexpression of FYN could significantly inhibit malignant tumor behaviors and promote tumor cell apoptosis.\nCONCLUSION: Thus, FYN may be central to the development of LIHC and maybe a novel biomarker for clinical diagnosis and treatment.", "claims": [{"id": "claim-method", "statement": "Kaplan–Meier analysis and the log-rank test were used to compare the survival probabilities between different groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35397600", "locator": "sections[12] \"Statistical Analysis\" paragraph 2", "quote": "Kaplan–Meier analysis and the log-rank test were used to compare the survival probabilities between different groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All gene expression profiles of LIHC are obtained from the TCGA database (portal.gdc.cancer.gov/projects/TCGA-LIHC) and GEO database (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25097). Other data used to support the findings of this study are within this article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35397600", "locator": "sections[28] \"Availability of data and materials\" paragraph 2", "quote": "All gene expression profiles of LIHC are obtained from the TCGA database (portal.gdc.cancer.gov/projects/TCGA-LIHC) and GEO database (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25097). Other data used to support the findings of this study are within this article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified ten hub genes in the protein–protein interaction (PPI) network, but only three (COLEC10, TGFBR3, and FYN) appeared closely related to the prognosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35397600", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified ten hub genes in the protein–protein interaction (PPI) network, but only three (COLEC10, TGFBR3, and FYN) appeared closely related to the prognosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified ten hub genes in the protein–protein interaction (PPI) network, but only three (COLEC10, TGFBR3, and FYN) appeared closely related to the prognosis.", "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:35397600"], "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:GSE25097"], "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:GSE25097"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35397600", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12885-022-09388-5", "sha256": "sha256:30442ff46c663329b322dafa52297b2344223787ce9fb0f216f89c28acddb93c", "bytes": 33849, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12885-022-09388-5", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8994319", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE25097", "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=GSE25097", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25097", "version": null, "note": "All gene expression profiles of LIHC are obtained from the TCGA database (portal.gdc.cancer.gov/projects/TCGA-LIHC) and GEO database (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25097). Other data used to support the findings of this study are within this article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All gene expression profiles of LIHC are obtained from the TCGA database (portal.gdc.cancer.gov/projects/TCGA-LIHC) and GEO database (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25097). 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"R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE25097"], "resolved_accessions": ["GSE25097"], "statements": ["All gene expression profiles of LIHC are obtained from the TCGA database (portal.gdc.cancer.gov/projects/TCGA-LIHC) and GEO database (www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25097). Other data used to support the findings of this study are within this article."], "basis": "The paper names GSE25097 in GEO database and the accession resolves in the repository. 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