The Cancer Genome Anatomy Projects Genetic Annotation Initiative

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One focus of the Bioinformatics Core has been to expand the functionality of existing display tools. The Protein Structure Viewer has two components: one displays amino acid alterations on the global structure of a protein; the second displays these alterations on three-dimensional protein structures. This application has been modified to display nonsense and frameshift mutations, and has been integrated with the Cancer Genome WorkBench. The LPGImage application (http://lpgimage.nci.nih.gov/LPGimage/) serves to display tissue microarray (TMA) data generated by Dr. Jin Jens laboratory. The Core has modified the application to display new data: computer assisted protein expression scoring. The number of antibodies in the TMA database has been increased to 81. In addition, the Bioinformatics Core is playing a leading role in the development of caLIMS2, a open-source, caBIG-compliant laboratory information management system (http://gforge.nci.nih.gov/projects/calims2/). caLIMS2 will function both as an information management system and a link between caBIG-compliant data repositories and analytical tools. The version 0.5 milestone 1 release has been completed. Finally, the Core provides informatics support to laboratories in the LPG and their collaborators. Projects supported by the Bioinformatics Core include a genomewide association study of liver cancer (Buetow Lab), identification of gene expression profiles in the NCI60 cancer cell lines (Buetow and Monks Labs), the identification of TGF-beta responsive genes in breast cancer (Lee and Wakefield Labs), the identification of TAF1 and TAF7 targets (Buetow, Lee and Singer Labs) and the investigation of genomic alterations in esophageal cancer (Lee and Taylor Labs).