1st International and 10th National Iranian Conference on Bioinformatics

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Integrative analysis of protein-coding genes, long non-coding genes, and microRNAs in breast cancer by GDC RNATOOLS and drug-gene interaction analysis

Paper ID : 1220-ICB10

Authors:

Romina Norouzi¹, Sajjad Gharaghani *²

¹پردیس کیش دانشگاه تهران

²دانشگاه تهران

Abstract:

Introduction: For this study, all mRNAs (Gene Expression Quantification (and microRNAs (BCGSC miRNA Profiling) count matrix (1204 samples and 60483genes for mRNAs and 1182 samples and 2588genes for microRNAs) data for breast cancer (the primary tumor) get from TCGA by GDC client after that normalized by TMM method and finding out differential express genes by Deseq2 package. Volcano plot and bar plot and Hierarchical clustering are used to visualize DEGS analysis results.
For ceRNAs network analysis of internally incorporated databases of miRNA-mRNA and miRNA-lncRNA interactions are used. lncRNA-miRNA-mRNA interactions reported and visualized in Cytoscape. For Functional enrichment analysis, perform Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Disease Ontology (DO) on the list of DEGs.
to find drug-gene interaction, by using DGIdb, selected (up and downregulated) gene in DEG file with criteria (logFC>2 and adjP.Val >0.005) for up-regulated and (logFC<-2 and adjP.Val >0.005) for the downregulated gene) and the results used as input for the DGIdb database. Then the interactions between drugs and differential express genes and the list of interactions are used as input to generate a network of genes and drugs.
Results: Based on analysis 1763 differential express genes find out in breast cancer which among them 1514 are protein-coding, 191 are lncRNAs and noncoding RNAs, and 47 pseudogenes and 4 TR and 7 TEC gens and 2 IG genes. Based on ceRNAs network analysis finding 404 miRNAs sponges by 404 lncRNAs, and 404 miRNAs directly interact with 404 mRNAs.
Drug -gene interaction prediction by DGIdb: based on the filter that is set on DEGs, find 606 downregulated genes that interact with the same number of drugs such as HRITONAVIREPARIN, CISPLATIN, RITONAVIR, etc. and 73 upregulated genes interact with the same numbers of drugs such as METHOTREXATE, TRASTUZUMAB, and so on.

Keywords:

Keywords: GDCRNA; lncRNAs, circulating RNA, breast cancer, drug-gene interaction, DGIdb

Status : Paper Accepted (Poster Presentation)