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BRCAbase: a breast cancer functional genomics resource
David Sims, Borisas Bursteinas, Qiong Gao, Ekta Jain, Alan MacKay, Costas Mitsopoulos, Marketa Zvelebil
Breakthrough Breast Cancer Research Centre, The Institute of Cancer Research, London, UK
The heterogeneity of breast cancer pathology and response to treatment has instigated a wide range of molecular profiling approaches to attempt to stratify breast cancer subtypes and patterns of genomic rearrangement. More recently, RNAi and drug screens have aimed to identify new molecular targets and therapeutics. However, gene-specific data from large-scale studies is often difficult to access from supplementary material or microarray data repositories, and many functional genomic studies generate datasets that can be mined in a number of different ways from those originally published.
We have developed BRCAbase (brcabase.icr.ac.uk) to provide a unique, publicly accessible resource for the analysis and integration of breast cancer functional genomic datasets. BRCAbase provides a simple online interface for the navigation, cross-linking and cross-correlation of gene expression, aCGH and RNAi screen data from breast cancer cell lines and tumour samples. BRCAbase enables the interrogation of large gene lists in the context of statistically analysed functional genomic datasets, protein interaction networks, pathways, GO terms, somatic mutations and drug targets. It provides interactive visualisations of gene expression, aCGH and RNAi datasets as well as interaction networks. BRCAbase collates data from a wealth of breast cancer molecular profiling and functional screening studies into a single portal, where analysed and annotated results can be accessed at the level of a single gene, sample or study. Thus, BRCAbase enables breast cancer researchers to quickly assess the potential significance of genes of interest in the context of prior knowledge in the field.
