Bioinformatics Analysis Explores Potential Hub Genes in Nonalcoholic Fatty Liver Disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34777484", "kind": "science-record", "revision": 4, "content_hash": "sha256:b59c345e676bf365a5a85d70397a56f2bdb7fdcb3322b66debf3484f55d45379", "created_at": "2026-11-01T17:36:28Z", "updated_at": "2026-11-01T22:05:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Analysis Explores Potential Hub Genes in Nonalcoholic Fatty Liver Disease.", "doi": "10.3389/fgene.2021.772487", "pmid": "34777484", "authors": ["Chutian Wu", "Yun Zhou", "Min Wang", "Guolin Dai", "Xiongxiu Liu", "Leizhen Lai", "Shaohui Tang"], "journal": "Frontiers in genetics", "year": 2021, "abstract": "Background: Nonalcoholic fatty liver disease (NAFLD) is now recognized as the most prevalent chronic liver disease worldwide. However, the dysregulated gene expression for NAFLD is still poorly understood. Material and methods: We analyzed two public datasets (GSE48452 and GSE89632) to identify differentially expressed genes (DEGs) in NAFLD. Then, we performed a series of bioinformatics analyses to explore potential hub genes in NAFLD. Results: This study included 26 simple steatosis (SS), 34 nonalcoholic steatohepatitis (NASH), and 13 healthy controls (HC). We observed 6 up- and 19 down-regulated genes in SS, and 13 up- and 19 down-regulated genes in NASH compared with HC. Meanwhile, the overlapping pathways between SS and NASH were PI3K-Akt signaling pathway and pathways in cancer. Then, we screened out 10 hub genes by weighted Gene Co-Expression Network Analysis (WGCNA) and protein-protein interaction (PPI) networks. Eventually, we found that CYP7A1/GINS2/PDLIM3 were associated with the prognosis of hepatocellular carcinoma (HCC) in the TCGA database. Conclusion: Although further validation is still needed, we provide useful and novel information to explore the potential candidate genes for NAFLD prognosis and therapeutic options.", "claims": [{"id": "claim-method", "statement": "Considering that GSE89632 had more comprehensive and complete data, we used GSE89632 to detect modules highly correlated with NAFLD, and WGCNA was performed using R package “WGCNA” and carried out on all genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34777484", "locator": "sections[6] \"Weighted Gene Co-Expression Network Analysis\" paragraph 2", "quote": "Considering that GSE89632 had more comprehensive and complete data, we used GSE89632 to detect modules highly correlated with NAFLD, and WGCNA was performed using R package “WGCNA” and carried out on all genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34777484", "locator": "sections[18] \"Data Availability Statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 10 NAFLD hub genes and found that CYP7A1, GINS2, and PDLIM3 were associated with hepatocellular carcinoma prognosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34777484", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Then, we screened out 10 hub genes by weighted Gene Co-Expression Network Analysis (WGCNA) and protein-protein interaction (PPI) networks."}, {"asset": "source:pmid:34777484", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Eventually, we found that CYP7A1/GINS2/PDLIM3 were associated with the prognosis of hepatocellular carcinoma (HCC) in the TCGA database."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study identified 10 NAFLD hub genes and found that CYP7A1, GINS2, and PDLIM3 were associated with hepatocellular carcinoma 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:34777484"], "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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