ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes.

ABSTRACT: ChIP-on-chip has emerged as a powerful tool to dissect the complex network of regulatory interactions between transcription factors and their targets. However, most ChIP-on-chip analysis methods use conservative approaches aimed at minimizing false-positive transcription factor targets. We present a model with improved sensitivity in detecting binding events from ChIP-on-chip data. Its application to human T cells, followed by extensive biochemical validation, reveals that 3 oncogenic transcription factors, NOTCH1, MYC, and HES1, bind to several thousand target gene promoters, up to an order of magnitude increase over conventional analysis methods. Gene expression profiling upon NOTCH1 inhibition shows broad-scale functional regulation across the entire range of predicted target genes, est

SUBMITTER: Margolin AA 

PROVIDER: S-EPMC2613038 | biostudies-literature | 2009 Jan

REPOSITORIES: biostudies-literature