We are pleased to announce two new ENCODE 3 transcription factor binding site track sets for human (GRCh37/hg19, GRCh38/hg38). These track sets show regions of transcription factor binding derived from a large collection of ChIP-seq experiments performed by the ENCODE project between February 2011 and November 2018.
The ENCODE TF ChIP-seq data were processed using the
ENCODE Transcription Factor ChIP-seq Processing Pipeline to generate peaks of TF binding.
Peaks from 1264 experiments (1256 in hg38) representing 338 transcription factors (340 in hg38) in
130 cell types (129 in hg38) were used to generate these two track sets.
An example of these two track sets is shown in the following sessions where CTCF binds to the MYC Proto-Oncogene
-across more than 100 cell types. CTCF is a transcription factor identified as a repressor of MYC
+across a few selected cell types. CTCF is a transcription factor identified as a repressor of MYC
shown to inhibit cell growth (Qi et al., 2002).
Thanks to the ENCODE Consortium, the ENCODE ChIP-seq production laboratories, and the ENCODE Data Coordination Center for generating and processing the TF ChIP-seq datasets. The ENCODE accession numbers of the constituent datasets are available on the peak details page as links in the Clusters tracks and in the track title for the Peaks tracks. Special thanks to Henry Pratt, Jill Moore, Michael Purcaro, and Zhiping Weng, PI, at the ENCODE Data Analysis Center (ZLab at UMass Medical Center) for providing the peak datasets, metadata, and guidance developing these track sets. Thanks to Kate Rosenbloom and Conner Powell of the UCSC Genome Browser group for their work in creating and releasing these track sets.
- +A genome browser is now available for the Chinese Hamster Ovary cell line assembly released in June 2017 by the Eagle Genomics Ltd (CHOK1S_HZDv1).
A genome browser is now available for the Felis catus assembly released in November 2017 by the Genome Sequencing Center (GSC) at Washington University (WashU) School of Medicine (Felis_catus_9.0).