Bioinformatics identification of crucial genes and pathways associated with hepatocellular carcinoma
| Autor: | Xixi Wang, Xueren Gao, Shulong Zhang |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Male Crucial gene Carcinoma Hepatocellular Biophysics Biology Bioinformatics medicine.disease_cause Biochemistry Pathogenesis 03 medical and health sciences 0302 clinical medicine Valine medicine Humans Gene Regulatory Networks Protein Interaction Maps Molecular Biology Gene Survival analysis Research Articles ACACB Cyclin-dependent kinase 1 Liver Neoplasms Computational Biology Cell Biology hepatocellular carcinoma medicine.disease Microarray Analysis digestive system diseases Neoplasm Proteins Gene Expression Regulation Neoplastic 030104 developmental biology Gene Ontology 030220 oncology & carcinogenesis Hepatocellular carcinoma Female Carcinogenesis Transcriptome Software Research Article Pathway Signal Transduction |
| Zdroj: | Bioscience Reports |
| ISSN: | 1573-4935 0144-8463 |
| Popis: | Hepatocellular carcinoma (HCC) is a major cause of cancer-related death worldwide. Up to date, HCC pathogenesis has not been fully understood. The aim of the present study was to identify crucial genes and pathways associated with HCC by bioinformatics methods. The differentially expressed genes (DEGs) between 14 HCC tissues and corresponding non-cancerous tissues were identified using limma package. Gene Ontology (GO) and KEGG pathway enrichment analysis of DEGs were performed by clusterProfiler package. The protein–protein interaction (PPI) network of DEGs was constructed and visualized by STRING database and Cytoscape software, respectively. The crucial genes in PPI network were identified using a Cytoscape plugin, CytoNCA. Furthermore, the effect of the expression level of the crucial genes on HCC patient survival was analyzed by an interactive web-portal, UALCAN. A total of 870 DEGs including 237 up-regulated and 633 down-regulated genes were identified in HCC tissues. KEGG pathway analysis revealed that DEGs were mainly enriched in complement and coagulation cascades pathway, chemical carcinogenesis pathway, retinol metabolism pathway, fatty acid degradation pathway, and valine, leucine and isoleucine degradation pathway. PPI network analysis showed that CDK1, CCNB1, CCNB2, MAD2L1, ACACB, IGF1, TOP2A, and EHHADH were crucial genes. Survival analysis suggested that the high expression of CDK1, CCNB1, CCNB2, MAD2L1, and TOP2A significantly decreased the survival probability of HCC patients. In conclusion, the identification of the above crucial genes and pathways will not only contribute to elucidating the pathogenesis of HCC, but also provide prognostic markers and therapeutic targets for HCC. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|