In the past year UCSC has focused on improving the accessibility and usability of the ENCODE data hosted in the Genome Browser. The ENCODE Analysis Working Group (AWG) reprocessed the transcription factor ChIP-seq and DNaseI HS peak call data sets released through March 2012 using the uniform processing pipeline developed for the ENCODE Integrative Analysis effort. This reprocessing factored out many of the cross-lab differences, allowing the different data sets to be used more effectively in the same analyses. These reprocessed data sets were released on the Genome Browser as the Transcription Factor ChIP-seq Uniform Peaks track (within the ENC TF Binding super-track) and the DNaseI Hypersensitivity Uniform Peaks track (within the ENC DNase/FAIRE super-track). The new data sets that met a specific integrated quality metric defined by the AWG (http://genome.ucsc.edu/ENCODE/qualityMetrics.html) were then used to update the individual Transcription Factor ChIP-seq Clusters and Digital DNaseI Hypersensitivity Clusters tracks within the ENCODE Integrated Regulation super-track set, providing summary clustered views. ENCODE data hosted in the Browser has now been fully accessioned through the Gene Expressions Omnibus (GEO) repository (21) and cross-linked
