Cancer Systems Biology, Bioinformatics and Medicine

Abstract

The amount of data generated in cancer research is growing rapidly. High-density array-based technologies, such as genome-wide single nucleotide polymorphism (SNP) genotyping and gene expression microarrays, are producing data that is not only larger in size, but also in complexity, with regard to study design and associated meta-data. This chapter discusses how the flood of genomic and transcriptomic data is managed in databases, often by large collaborative consortia developing new approaches in informatics to maximize the availability and utility of data. Genetic variation databases are most often designed for a particular layer of detail, such as single disease-causing variants associated with specific phenotypes; databases for genome-wide variation, both for SNPs and structural variants; and large repositories for complete genome-wide association studies. Gene-expression microarray data is stored in large repositories, and new services have been developed that take advantage of the increasing number and diversity of stored experiments. By associating data with biological information and integrative analysis, it can be transformed from high dimensionality to a summary level that is directly usable by bench biologists.