Cyclin-dependent kinase inhibitor 3 (CDKN3) novel cell cycle computational network between human non-malignancy associated hepatitis/cirrhosis and hepatocellular carcinoma (HCC) transformation.

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However, the molecular network and interpretation of CDKN3 through the cell cycle between non-malignancy associated hepatitis/cirrhosis and hepatocellular carcinoma (HCC) have remained to be elucidated. Here, we have constructed and analysed significant high expression gene CDKN3 activated and inhibited cell cycle networks from 25 HCC versus 25 non-malignancy associated hepatitis/cirrhosis patients (viral infection HCV or HBV) in GEO Dataset GSE10140-10141, by combination of a gene regulatory network inference method based on linear programming, and decomposition procedure using CapitalBio MAS 3.0 software, based on integration of public databases including Gene Ontology, KEGG, BioCarta, GenMapp, Intact, UniGene, OMIM, and others. Comparing the same and differently activated and inhibited CDKN3 networks with GO analysis, between non-malignancy associated hepatitis/cirrhosis and HCC, our results suggest a CDKN3 cell cycle network (i) with stronger DNA replication and with weaker ubiquitin-dependent protein catabolism as common characteristics in both non-malignancy associated hepatitis/cirrhosis and HCC; (ii) with more cell division and weaker mitotic G2 checkpoint in non-malignancy associated hepatitis/cirrhosis; (iii) with stronger cell cycle and weaker cytokinesis, as a result forming multinucleate cells in HCC. Thus, it is useful to identify CDKN3 cell cycle networks for comprehension of molecular mechanism between non-malignancy associated hepatitis/cirrhosis and HCC transformation.", "claims": [{"id": "claim-target-result", "statement": "Using gene regulatory network inference based on linear programming and decomposition with CapitalBio MAS 3.0 on 25 HCC versus 25 hepatitis/cirrhosis cases from GEO GSE10140‐10141, the study found common stronger DNA replication and weaker ubiquitin‐dependent protein catabolism, while the networks differed in cell division, mitotic G2 checkpoint, cell cycle, and cytokinesis between hepatitis/cirrhosis and HCC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:21535270", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Here, we have constructed and analysed significant high expression gene CDKN3 activated and inhibited cell cycle networks from 25 HCC versus 25 non‐malignancy associated hepatitis/cirrhosis patients (viral infection HCV or HBV) in GEO Dataset GSE10140‐10141, by combination of a gene regulatory network inference method based on linear programming, and decomposition procedure using CapitalBio MAS 3.0 software, based on integration of public databases including Gene Ontology, KEGG, BioCarta, GenMapp, Intact, UniGene, OMIM, and others."}, {"asset": "source:pmid:21535270", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Comparing the same and differently activated and inhibited CDKN3 networks with GO analysis, between non‐malignancy associated hepatitis/cirrhosis and HCC, our results suggest a CDKN3 cell cycle network (i) with stronger DNA replication and with weaker ubiquitin‐dependent protein catabolism as common characteristics in both non‐malignancy associated hepatitis/cirrhosis and HCC; (ii) with more cell division and weaker mitotic G2 checkpoint in non‐malignancy associated hepatitis/cirrhosis; (iii) with stronger cell cycle and weaker cytokinesis, as a result forming multinucleate cells in HCC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Using gene regulatory network inference based on linear programming and decomposition with CapitalBio MAS 3.0 on 25 HCC versus 25 hepatitis/cirrhosis cases from GEO GSE10140‐10141, the study found common stronger DNA replication and weaker ubiquitin‐dependent protein catabolism, while the networks differed in cell division, mitotic G2 checkpoint, cell cycle, and cytokinesis between hepatitis/cirrhosis and HCC.", "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:21535270"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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