1st International and 10th National Iranian Conference on Bioinformatics
Home Accepted Papers
Discovering potential hub genes in gastric cancer using in silico analysis
Paper ID : 1049-ICB10
Authors:
محمد حسین حبیبی *1, آتنا سادات حسینی2, سارا رضی3
1دانشگاه تخصصی فناوری های نوین آمل
2دانشگاه آزاد اسلامی شهر ری واحد یادگار امام
3بنیانگذار و مدیریت موسسه پیشگامان علوم نوین ویرا
Abstract:
Gastric cancer was responsible for 7.7% of total cancer death worldwide in 2020[1]. This research aims to discover hub genes and potential drug targets in Gastric cancer using systems biology approaches. Three sets of microarray profiles, including GSE79973, GSE13911, GSE54129, were downloaded from Gene Expression Omnibus (GEO) and analyzed through R programming (Bioconductor package including limma, affy, and oligo libraries). Differentially expressed genes (DEGs) were filtered with P_val < 0.05, Log Fc > 1, and Log Fc <-1, then a total of 217 overlapped genes (143 downregulated and 74 upregulated) were extracted, and a PPI network was constructed using Cytoscape software. Firstly, three subnetworks were identified with the MCODE plugin based on connectivity. After merging three subnetworks, 35 resulting genes were transferred to the Enricher database for enrichment analysis. The analysis was performed in four groups: the KEGG pathway, GO cell components, GO molecular functions and GO Biological process. The first result for each group was protein digestion and absorption, collagen-containing extracellular matrix, platelet-derived growth factor binding and, extracellular matrix organization, respectively. In the next step, centrality analysis with a focus on degree and betweenness was performed on overlapped genes through centiscape 2.2 plugin. The five top genes with the highest betweenness were FN1, MUC5AC, PTGS2, ATP4A, and CXCL8 and the five top genes with the highest degree were FN1, COL1A1, COL1A2, THBS2, and TIMP1.
Keywords:
Gastric cancer; systems biology; microarray profiles; differentially expressed genes; enrichment analysis
Status : Paper Accepted (Poster Presentation)