title: In silico analysis of differential gene expressions in biliary stricture and hepatic carcinoma.
abstract: In-silico attempt was made to identify the key hub genes which get differentially expressed in biliary stricture and hepatic carcinoma. Gene expression data, GSE34166, was downloaded from the GEO database, which contains 10 biliary stricture samples (4 benign control and 6 malignant carcinoma), for screening of key hub genes associated with the disease. R packages scripts were identified 85 differentially expressed genes. Further these genes were uploaded in WebGestalt database and identified nine key genes. Using STRING database and Gephi software, the protein-protein interaction networks were constructed and also studied gene ontology through WebGestalt. Finally, we identified four key genes (CXCR4, ADH1C, ABCB1 and ADH1A) are associated with liver carcinoma and further cross-validated with Liverome, Protein Atlas database and bibliography. In addition, transcription factors and their binding sites also studied. These identified hub genes and their transcription factors are the probable potential targets for possible future drug design.
authors: Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa 516003, Andhra Pradesh, India. Electronic address: mkgupta.bioinfo@gmail.com.
authors: Manoj Kumar
authors: MK
authors: Gupta
authors: Biomedical Informatics Centre, Regional Medical Research Centre (ICMR), Bhubaneswar 751023, Odisha, India. Electronic address: bioinfo.santosh@gmail.com.
authors: Santosh Kumar
authors: SK
authors: Behara
authors: Department of Biotechnology & Bioinformatics, Yogi Vemana University, Kadapa 516003, Andhra Pradesh, India. Electronic address: vrkrishna70@gmail.com.
authors: Ramakrishna
authors: R
authors: Vadde
mesh_terms: D018435:ATP Binding Cassette Transporter, Subfamily B / Q000235:genetics / Q000378:metabolism; D000426:Alcohol Dehydrogenase / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D006528:Carcinoma, Hepatocellular / Q000235:genetics*; D002760:Cholangiopancreatography, Endoscopic Retrograde; D002779:Cholestasis / Q000235:genetics*; D003198:Computer Simulation; D003251:Constriction, Pathologic / Q000235:genetics; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D063990:Gene Ontology; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics*; D025941:Protein Interaction Mapping / Q000379:methods; D019718:Receptors, CXCR4 / Q000235:genetics / Q000378:metabolism
chemical_list: C513055:ABCB1 protein, human; D018435:ATP Binding Cassette Transporter, Subfamily B; C527276:CXCR4 protein, human; D019718:Receptors, CXCR4; C489332:ADH1B protein, human; C420272:ADH1C protein, human; D000426:Alcohol Dehydrogenase
keywords: Biliary strictures; Differentially expressed genes; Gene Expression Omnibus; Hub genes; Liver carcinoma; Microarray analysis; Transcription factors