Construction and analysis of regulatory networks in breast cancer

Master of Philosophy in Computer Science 2014-2015 EXT Elizabeth Sherly Umesh P
(Dept. of Computational Biology and Bioinformatics )
"Dept. of Computational Biology and Bioinformatics
University of Kerala"

Breast cancer is a complex and heterogeneous disease having different pathological
conditions. Identification of genes associated with breast cancer provides helpful information which can be used for providing better treatment and personalized medicines.Numerous methodologies are now available to examine the genes regulated by breast cancer. Recent advances in Bioinformatics have enabled to analyze the data obtained from various sources such as microarray, ChIP-Seq, RNA-Seq etc. Analyses of the differential expression obtained from RNA-Seq data provide useful information for the construction and analysis of biological networks. For this work, six RNA-Seq control cell lines data obtained from NCBI (a public repository) have been analyzed to obtain the differential expression using the standard RNA-seq pipeline. GFold is used to get the rank of differentially expressed genes. Common up-regulated and down-regulated genes in all the cell lines and uniquely regulated genes in each cell line has been annotated using DAVID and WebGestalt for biological interpretations. Inferring of KEGG pathway and gene ontologies of regulated genes (up and down) gives some interesting results. Regulation of action cytoskeleton, MAPK signaling, wnt signaling, VEGF signaling pathway, cell adhesion molecules are the pathways significantly over represented in up-regulated genes. Cytokine-cytokine receptor interaction, Neuroactive ligand-receptor interaction are the pathways significantly associated with down-regulated genes.