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Online Journal of Bioinformatics

Volume 11 (1): 83-89, 2010

Brain tumor biomarker identification via differential gene expression analysis of microarray data using CGAP.


Ravichandran S, Jeyakumar N


Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore 641 046, INDIA.





Ravichandran S, Jeyakumar N, Brain tumor biomarker identification via differential gene expression analysis microarray data using CGAP, Onl J Bioinform, 11 (1): 83-89, 2010. The Cancer Genome Anatomy Project (CGAP), a cancer microarray database and data-mining platform contains the entire dataset from more than 20 different types of cancer microarray data sets published to date in worldwide scientific literature. We undertook a meta-analysis via CGAP, in an attempt to identify potentially drugable brain tumor therapeutic targets, which are over-expressed in cancer tissue compared to normal brain tissue. The data mining platform Digital Gene Expression Displayer (DGED) of CGAP was used for differential gene expression analysis of brain cancer tissue and normal brain tissue utilizing sequence odds ratio and measure of significance. The result contains 2298 up regulated genes in brain tumor tissues. The functional annotation of differentially expressed genes using gene ontology database, we found five enriched GO categories in up regulated genes. On further analysis of one of enriched functional category ‘Transcription Factor Activity’ which includes 75 genes using KEGG pathway database we identified five genes namely TCF7L1,RXRA,RXRG,RB1, and NFATC3, which were previously implicated in cancer pathways. These genes may be considered as biomarkers for brain tumors and will be interesting to investigate experimentally.


Keywords: Brain tumor, Differential gene expression, CGAP, DGED, Biomarkers