13 May 2013 - Uniform Peaks of Transcription Factor ChIP-seq from ENCODE/Analysis
UCSC has released a new browser track containing 690 datasets of transcription factor ChIP-seq
peaks based on data from all five ENCODE TFBS ChIP-seq production groups from the project
inception in 2007 through the ENCODE March 2012 data freeze.
The track covers 161 unique regulatory factors (generic and sequence-specific factors),
spanning 91 human cell types, some under various treatment conditions.
Transcription Factor ChIP-seq Uniform Uniform Peaks from ENCODE/Analysis
File selection tool
This track represents peak calls (regions of enrichment) generated by the ENCODE Analysis Working
Group (AWG) using the uniform processing pipeline developed for the ENCODE Integrative Analysis
effort and published in a set of coordinated papers in September 2012. Peak calls from that
effort (based on datasets from the January 2011 ENCODE data freeze) are available at the
ENCODE Analysis Data Hub.
The new Uniform TFBS track at UCSC includes newer data, slightly modified processing methods,
and improved metadata. Quality metrics are included in metadata, with detailed metrics in a
quality spreadsheet linked to the track description.
Browser users will see the uniform peaks first when using track search for TFBS, and
this track is now the default track shown when the ENCODE TF Binding menu item is
selected in the browser.
The primary and lab-processed data (along with methods descriptions, credits and references)
on which this track is based are available in the following ENCODE tracks: HAIB TFBS, SYDH TFBS,
UChicago TFBS, UTA TFBS, UW CTCF Binding. Many thanks to Anshul Kundaje of the ENCODE AWG
for providing the uniform peaks data, description, and quality spreadsheets.
7 April 2013 - User Resources and Frequently Asked Questions page added to website
This new page provides links to
ENCODE informational material and tools at the NHGRI,
GEO, UCSC, and Nature, together with links to some of the most useful pages at encodeproject.org.
It also includes a helpful FAQ section culled from ENCODE questions received on the ENCODE and
Genome Browser mailing lists.
25 January 2013 - Uniform DNaseI Hypersensitivity sites from ENCODE Analysis Working Group
The ENCODE Analysis Working Group (AWG) has performed uniform processing
on datasets produced by multiple data production groups in the ENCODE
The AWG uniform datasets are used in downstream analysis pipelines by
members of the ENCODE Consortium and are one of the primary sources of
data referenced in the 2012 ENCODE integrative analysis.
UCSC has released a new browser track and a track update based on the AWG uniform processing of
ENCODE DNaseI data.
28 September 2012 - New ENCODE on-line tutorial and Quick Reference Cards
To supplement the existing ENCODE Foundations tutorial, OpenHelix has developed a second
tutorial describing newer ENCODE data and access tools.