title: Cyclin-dependent kinase inhibitor 3 (CDKN3) novel cell cycle computational network between human non-malignancy associated hepatitis/cirrhosis and hepatocellular carcinoma (HCC) transformation.
abstract: The relationship of cyclin-dependent kinase inhibitor 3 (CDKN3) with tumours has previously been presented in a number of publications. 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.
authors.affiliation: Biomedical Center, School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, China. wanglin98@tsinghua.org.cn
authors.forename: L
authors.initials: L
authors.lastname: Wang
authors.forename: L
authors.initials: L
authors.lastname: Sun
authors.forename: J
authors.initials: J
authors.lastname: Huang
authors.forename: M
authors.initials: M
authors.lastname: Jiang
mesh_terms: D000465:Algorithms; D006528:Carcinoma, Hepatocellular / Q000378:metabolism*; D002453:Cell Cycle; D019295:Computational Biology / Q000379:methods; D050756:Cyclin-Dependent Kinase Inhibitor Proteins / Q000378:metabolism*; D054637:Dual-Specificity Phosphatases / Q000378:metabolism*; D005355:Fibrosis / Q000378:metabolism*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006505:Hepatitis / Q000378:metabolism*; D006801:Humans; D008113:Liver Neoplasms / Q000378:metabolism*; D008954:Models, Biological; D016571:Neural Networks, Computer; D020411:Oligonucleotide Array Sequence Analysis
chemical_list: D050756:Cyclin-Dependent Kinase Inhibitor Proteins; C084429:CDKN3 protein, human; D054637:Dual-Specificity Phosphatases