This directory contains the downloadable files associated with the ENCODE 
Regulation 'Txn Factor' track.  All data in this track are freely available.

This track is described here:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3

ENCODE data files are subject to use restrictions for 9 months following data 
submission (http://genome.ucsc.edu/ENCODE/terms.html).  All data in this track
have passed the 9 month restriction period and so are freely available.

The files listed below are provided for download.  See http://genome.ucsc.edu/FAQ/FAQformat.html
for format details.

Data files for this release:

* wgEncodeRegTfbsClusteredV3.bed.gz - TFBS clusters (V3) from ENCODE data uniformly processed by the ENCODE Analysis Working Group (BED 5+2 'factorSource' format. Has 2 list fields for cell ids and scores.  See track description for details)
* wgEncodeRegTfbsClusteredInputsV3.tab.gz - Auxiliary table with metadata for the clusters, describing each input experiment
* wgEncodeRegTfbsClusteredWithCellsV3.bed.gz - TFBS clusters together with input cell sources (BED 5+1 format: standard 5 fields of BED followed by comma-separated list of cell types)
* wgEncodeRegTfbsCellsV3.tab.gz - Auxiliary table showing single-letter abbreviation for each cell type used in input experiments (displayed in browser display)

Data files from the previous release of this track:

* wgEncodeRegTfbsClusteredV2.bed.gz - TFBS clusters (V2) from uniform processing of data from Jan. 2011 data freeze, with minor corrections
* wgEncodeRegTfbsClusteredInputs.tab.gz - Auxiliary table for V2
* wgEncodeRegTfbsCells.tab.gz - Auxiliary metadata table for V2

Script file:

* clusterAddSources.pl - used to generate *ClusteredWithCellsV*.bed file from *ClusteredV*.bed (or filtered clusters output from Table Browser) and *InputsV*.bed file.