FISH Oracle: a web server for flexible visualization of DNA copy number data in a genomic context

We have developed a web-based software FISH Oracle to visualize data from multiple array CGH experiments in a genomic context. Its fast visualization engine and advanced web and database technology supports highly interactive use. FISH Oracle comes with a convenient data import mechanism, powerful search options for genomic elements (e.g. gene names or karyobands), quick navigation and zooming into interesting regions, and mechanisms to export the visualization into different high quality formats. These features make the software especially suitable for the needs of life scientists.FISH Oracle offers a fast and easy to use visualization tool for array CGH and SNP array data. It allows for the identification of genomic regions representing minimal common changes based on data from one or more experiments. FISH Oracle will be instrumental to identify candidate onco and tumor suppressor genes based on the frequency and genomic position of DNA copy number changes. The FISH Oracle application and an installed demo web server are available at http://www.zbh.uni-hamburg.de/fishoracle webcite.In the recent years, high resolution genomic tiling arrays and SNP chips have become the standard technology to analyze copy number variations in cancer genomes. Modern arrays are inexpensive and allow for determining copy number changes at the resolution of individual genes. Gains or deletions of chromosomal material are often highly variable in size, ranging from several kilobases to entire chromosomes. One important strategy to reveal genetic loci containing putative cancer genes is to perform multiple experiments and identify chromosomal regions representing minimal common alterations. Since large alterations spanning many megabases are typically more common than the small ones containing only a few genes, as many experiments as possible should be included into such kind of analysis. Public databases like the Stanford Microarray Database [1], ArrayExpress [2], the caArray Data Port