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Colloquium - Wang

Transcriptional Regulatory Networks and the UCSC Cancer Genomics Browser
Ting Wang
University of California, San Diego
3/31/2009
4:30pm-5:30pm

The evolutionary forces that establish and hone the network of target genes for transcription factors are largely unknown. We report here new evidence suggesting mobile element mediated transcription regulation is an ongoing process. Recent, species-specific mobile elements, in particular, endogenous retroviruses (ERVs), can actively shape transcriptional networks in a species-specific manner. Our studies show that invaluable treasures are hidden in the "junk" DNA, that these once foreign genetic materials are important evolutionary forces that impact our genome in a systematic manner, and that the connections one can make between mis-regulated mobile elements and human diseases provide a new avenue for disease investigation.

In addition we describe the UCSC Cancer Genomics Browser, a suite of web-based tools to integrate, visualize and analyze cancer genomics and clinical data. This browser displays a whole-genome-oriented view of genome-wide experimental measurements for individual and sets of samples alongside their associated clinical information. We demonstrate the capability of this browser with data from several published large cancer genomics studies, including The Cancer Genome Atlas project. The browser is also being used on confidential, prepublication data by multiple groups. This browser inherits and integrates the UCSC Genome Browser's existing rich set of human biology and genetics data to enhance the interpretability of the cancer genomics data.

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