Identification of Crucial Candidate Genes and Pathways in Glioblastoma Multiform by Bioinformatics Analysis

• Published in: Biomolecules (Basel, Switzerland) Vol. 9; no. 5; p. 201
• Main Authors: Alshabi, Ali Mohamed, Vastrad, Basavaraj, Shaikh, Ibrahim Ahmed, Vastrad, Chanabasayya
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI 24.05.2019; MDPI AG
• Subjects: Brain Neoplasms - genetics; differential gene expression; Gene Expression Regulation, Neoplastic; Gene Regulatory Networks; Glioblastoma - genetics; glioblastoma multiform; Humans; MicroRNAs - genetics; MicroRNAs - metabolism; miRNA-target gene network; RNA, Messenger - genetics; RNA, Messenger - metabolism; TF-target gene network; topology analysis; Transcriptome; differential gene expression; topology analysis; glioblastoma multiform; TF-target gene network; miRNA-target gene network
• ISSN: 2218-273X; 2218-273X
• DOI: 10.3390/biom9050201

The present study aimed to investigate the molecular mechanisms underlying glioblastoma multiform (GBM) and its biomarkers. The differentially expressed genes (DEGs) were diagnosed using the limma software package. The ToppGene (ToppFun) was used to perform pathway and Gene Ontology (GO) enrichment analysis of the DEGs. Protein-protein interaction (PPI) networks, extracted modules, miRNA-target genes regulatory network and TF-target genes regulatory network were used to obtain insight into the actions of DEGs. Survival analysis for DEGs was carried out. A total of 590 DEGs, including 243 up regulated and 347 down regulated genes, were diagnosed between scrambled shRNA expression and Lin7A knock down. The up-regulated genes were enriched in ribosome, mitochondrial translation termination, translation, and peptide biosynthetic process. The down-regulated genes were enriched in focal adhesion, VEGFR3 signaling in lymphatic endothelium, extracellular matrix organization, and extracellular matrix. The current study screened the genes in the PPI network, extracted modules, miRNA-target genes regulatory network, and TF-target genes regulatory network with higher degrees as hub genes, which included , and . Survival analysis indicated that the high expression of and were predicting longer survival of GBM, while high expression of and were predicting shorter survival of GBM. High expression of and were associated with pathogenesis of GBM, while low expression of was associated with pathogenesis of GBM. In conclusion, the current study diagnosed DEGs between scrambled shRNA expression and Lin7A knock down samples, which could improve our understanding of the molecular mechanisms in the progression of GBM, and these crucial as well as new diagnostic markers might be used as therapeutic targets for GBM.