Bioinformatics-based screening of key genes for transformation of liver cirrhosis to hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32000807", "kind": "science-record", "revision": 7, "content_hash": "sha256:fecb3a2323a6d2ce88cb5957d20ab2935086cd6b30f5feac4ad99ed589e7cbad", "created_at": "2026-11-01T15:40:55Z", "updated_at": "2026-11-01T22:01:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics-based screening of key genes for transformation of liver cirrhosis to hepatocellular carcinoma.", "doi": "10.1186/s12967-020-02229-8", "pmid": "32000807", "authors": ["Chen Hao Jiang", "Xin Yuan", "Jiang Fen Li", "Yu Fang Xie", "An Zhi Zhang", "Xue Li Wang", "Lan Yang", "Chun Xia Liu", "Wei Hua Liang", "Li Juan Pang", "Hong Zou", "Xiao Bin Cui", "Xi Hua Shen", "Yan Qi", "Jin Fang Jiang", "Wen Yi Gu", "Feng Li", "Jian Ming Hu"], "journal": "Journal of translational medicine", "year": 2020, "abstract": "BACKGROUND: Hepatocellular carcinoma (HCC) is the most common type of liver tumour, and is closely related to liver cirrhosis. Previous studies have focussed on the pathogenesis of liver cirrhosis developing into HCC, but the molecular mechanism remains unclear. The aims of the present study were to identify key genes related to the transformation of cirrhosis into HCC, and explore the associated molecular mechanisms.\nMETHODS: GSE89377, GSE17548, GSE63898 and GSE54236 mRNA microarray datasets from Gene Expression Omnibus (GEO) were analysed to obtain differentially expressed genes (DEGs) between HCC and liver cirrhosis tissues, and network analysis of protein-protein interactions (PPIs) was carried out. String and Cytoscape were used to analyse modules and identify hub genes, Kaplan-Meier Plotter and Oncomine databases were used to explore relationships between hub genes and disease occurrence, development and prognosis of HCC, and the molecular mechanism of the main hub gene was probed using Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis.\nRESULTS: In total, 58 DEGs were obtained, of which 12 and 46 were up- and down-regulated, respectively. Three hub genes (CDKN3, CYP2C9 and LCAT) were identified and associated prognostic information was obtained. CDKN3 may be correlated with the occurrence, invasion, and recurrence of HCC. Genes closely related to changes in the CDKN3 hub gene were screened, and Kyoto Encyclopedia of Genes and Genomes (KEGGs) pathway analysis identified numerous cell cycle-related genes.\nCONCLUSION: CDKN3 may affect the transformation of liver cirrhosis into HCC, and represents a new candidate molecular marker of the occurrence and progression of HCC.", "claims": [{"id": "claim-method", "statement": "Survival-related hub genes were analysed using the Kaplan–Meier curve feature within the Kaplan–Meier Plotter database which included 364 cases of hepatocellular carcinoma (Fig. 3).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32000807", "locator": "sections[9] \"Selection and analysis of hub genes\" paragraph 2", "quote": "Survival-related hub genes were analysed using the Kaplan–Meier curve feature within the Kaplan–Meier Plotter database which included 364 cases of hepatocellular carcinoma (Fig. 3)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets during and/or analyzed during the current study available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32000807", "locator": "sections[21] \"notes\" paragraph 1", "quote": "The datasets during and/or analyzed during the current study available from the corresponding author on reasonable request."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:32000807"], "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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This gene was reported to be deleted, mutated, or overexpressed in several kinds of cancers"], ["CYP2C9", "Cytochrome P450 family 2 subfamily C member 9", "This gene encodes a member of the cytochrome P450 superfamily of enzymes. These monooxygenases catalyse many reactions involved in drug metabolism and the synthesis of cholesterol, steroids and other lipids"], ["LCAT", "Lecithin-cholesterol acyltransferase", "This gene encodes the extracellular cholesterol esterifying enzyme lecithin-cholesterol acyltransferase. Esterification of cholesterol is required for cholesterol transport"]], "row_count": 4, "column_count": 3, "numeric_cells": 3, "header_rows": 1, "locator": "section[9]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:32000807:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:064dc6748e5ce4b2ed28272c84628f3967b816f01a7de3990901cb74652fdc1e", "bytes": 1475, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#Tab2", "version": null, "note": "cBioPortal analysis of the 20 genes most closely related to CDKN3", "structure": {"pmcid": "PMC6993496", "section_index": 10, "section_title": "Screening and analysis of genes related to CDKN3 expression in HCC", "row_count": 21, "column_count": 5}, "table": {"label": "Table 2", "caption": "cBioPortal analysis of the 20 genes most closely related to CDKN3", "rows": [["Gene", "Cytoband", "Spearman’s correlation", "p-value", "q-value"], ["SPC25", "2q24.3", "0.86085851", "6.68E−111", "1.34E−106"], ["CDK1", "10q21.2", "0.85877853", "8.53E−110", "8.57E−106"], ["CCNB2", "15q22.2", "0.85556873", "4.02E−108", "2.69E−104"], ["NDC80", "18p11.32", "0.85377317", "3.33E−107", "1.67E−103"], ["DLGAP5", "14q22.3", "0.85123904", "6.27E−106", "2.52E−102"], ["CCNB1", "5q13.2", "0.84636895", "1.52E−103", "5.10E−100"], ["NCAPG", "4p15.31", "0.84493736", "7.38E−103", "2.12E−99"], ["CENPA", "2p23.3", "0.84378996", "2.59E−102", "6.50E−99"], ["TROAP", "12q13.12", "0.84327453", "4.53E−102", "1.01E−98"], ["TPX2", "20q11.21", "0.84187347", "2.05E−101", "4.12E−98"], ["KIF4A", "Xq13.1", "0.84112657", "4.57E−101", "8.34E−98"], ["CDCA3", "12p13.31", "0.83985708", "1.76E−100", "2.95E−97"], ["HJURP", "2q37.1", "0.83858943", "6.70E−100", "1.00E−96"], ["NUF2", "1q23.3", "0.83854781", "7.00E−100", "1.00E−96"], ["KIFC1", "6p21.32", "0.83732595", "2.51E−99", "3.36E−96"], ["PTTG1", "5q33.3", "0.83712825", "3.08E−99", "3.87E−96"], ["SKA1", "18q21.1", "0.83233493", "4.15E−97", "4.90E−94"], ["CDC25C", "5q31.2", "0.83159127", "8.75E−97", "9.76E−94"], ["NEK2", "1q32.3", "0.82993815", "4.54E−96", "4.80E−93"], ["SKA3", "13q12.11", "0.82253139", "5.87E−93", "5.89E−90"]], "row_count": 21, "column_count": 5, "numeric_cells": 83, "header_rows": 1, "locator": "section[10]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:32000807:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b262106e432f8a5020b0a0ee720e41a2e473f2ff9e2805dcf186a96a790bd333", "bytes": 1621, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#Tab3", "version": null, "note": "KEGG pathway enrichment analysis of CDKN3-related genes", "structure": {"pmcid": "PMC6993496", "section_index": 10, "section_title": "Screening and analysis of genes related to CDKN3 expression in HCC", "row_count": 9, "column_count": 4}, "table": {"label": "Table 3", "caption": "KEGG pathway enrichment analysis of CDKN3-related genes", "rows": [["Gene set name", "Count", "p-value", "Genes"], ["Cell cycle", "41", "9.93E−33", "E2F1, E2F2, CDC14B, DBF4, PKMYT1, TTK, PTTG2, CHEK1, PTTG1, CCNE2, CCNE1, CDC45, MCM7, CDKN2C, BUB1, ORC6, CCNA2, ORC1, CDC7, CDK1, CDC6, ESPL1, CDC20, MCM2, CDK4, CDC25C, MCM3, MCM4, MCM5, CDK2, CDC25A, MCM6, CDC25B, CCNB1, CCNB2, MAD2L1, PLK1, PCNA, BUB1B, ANAPC7, SMC1B"], ["DNA replication", "22", "3.25E−24", "LIG1, POLA1, POLA2, MCM2, RNASEH2A, MCM3, MCM4, MCM5, MCM6, RFC5, POLD3, PRIM1, DNA2, RFC3, RFC4, MCM7, POLE2, RFC2, POLD1, PRIM2, PCNA, FEN1"], ["Oocyte meiosis", "23", "2.35E−13", "CDK1, CPEB3, PKMYT1, AURKA, PTTG2, CDC20, ESPL1, PTTG1, CDC25C, PPP1CC, CDK2, CCNB1, CCNE2, CCNE1, MAD2L1, CCNB2, SGO1, PLK1, BUB1, FBXO43, FBXO5, ANAPC7, SMC1B"], ["Mismatch repair", "11", "2.00E−10", "EXO1, RFC5, POLD3, MSH6, RFC3, RFC4, RFC2, MSH2, LIG1, POLD1, PCNA"], ["Fanconi anaemia pathway", "13", "1.65E−08", "RAD51C, BLM, EME1, FAAP24, RMI2, BRCA1, RAD51, FANCI, FANCD2, FANCE, FANCG, UBE2T, FANCB"], ["Homologous recombination", "10", "5.51E−08", "POLD3, RAD51C, XRCC3, XRCC2, BLM, POLD1, EME1, RAD54B, RAD54L, RAD51"], ["Progesterone-mediated oocyte maturation", "14", "3.80E−06", "CCNB1, CDK1, MAD2L1, CCNB2, PLK1, CPEB3, BUB1, PKMYT1, ANAPC7, CDC25C, CCNA2, CDC25A, CDK2, CDC25B"], ["Spliceosome", "8", "7.94E−07", "SNRPA1, ALYREF, SNRPD1, SF3A2, SF3B4, RBMX, HNRNPU, SRSF3, HNRNPA3, SRSF9, USP39, SNRPB, SNRPA, SNRPF, THOC1,SNRPG, RBM17"]], "row_count": 9, "column_count": 4, "numeric_cells": 22, "header_rows": 1, "locator": "section[10]/table-wrap[2]#Tab3"}}], "gaps": ["asset:data:geo:GSE17548 not downloaded", "asset:data:geo:GSE17548 licence not read", "asset:data:geo:GSE54236 not downloaded", "asset:data:geo:GSE54236 licence not read", "asset:data:geo:GSE63898 not downloaded", "asset:data:geo:GSE63898 licence not read", "asset:data:geo:GSE89377 not downloaded", 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