Developing cancer genomic database and analyzing cancer datasets with integrating bioinformatic tools

Genome-wide profiles of tumors obtained using functional genomics platforms are being deposited to the public repositories at an astronomical scale, as a result of focused efforts by individual laboratories and large projects. Consequently, there is an urgent need for reliable tools that integrate and interpret these data in light of current knowledge and disseminate results to cancer researchers in a user-friendly manner. Here we aim to develop a bioinformatics platform to meet this need. The developed platform query functionalities are designed to fulfill most frequent analysis needs of cancer researchers with a view to generate novel hypotheses. It stores gene, protein and miRNA expression profiles, mutation information and copy number alterations for multiple cancer types, and proteinprotein interaction information. The platfom allows querying of results of primary analysis, integrative analysis and network analysis of oncogenomics data. The querying for primary analysis includes differential gene and miRNA expression as well as changes in gene copy number measured with SNP microarrays. It provides results of integrative analysis of gene expression profiles with copy number alterations, mutations, protein expressions and miRNA profiles as well as generalized integrative analysis using gene set enrichment analysis. The network analysis capability includes storage and visualization of gene co-expression, inferred gene regulatory networks and protein-protein interaction information. Finally, the platform provides correlations between gene expression and clinical outcomes in terms of univariate survival analysis.At present the platform provides different types of information extracted from 90 cancer genomics studies with information from more than 20,000 patients. The presence of multiple data types, novel integrative analysis for identifying regulators of oncogenesis, network analysis and ability to query gene lists/pathways are distinctive features of the platform. Finally, compared to current tools in the literature, the developed platform offers a novel bioinformatics platform to the community with it?s rich content.Key Words: Bioinformatics, Cancer, Integrative Analysis, Genetics, Gene Expression, Protein Expression, miRNA Expression, Gene Copy Number, Mutations