5948426ec1f630f4aa6d40ec40b87ae6ad2a13fb
kate
  Wed May 15 14:35:33 2019 -0700
Add informational paragraph (JK request) and notes about subtrack coloring. refs #23243

diff --git src/hg/makeDb/trackDb/human/encTfChipPk.html src/hg/makeDb/trackDb/human/encTfChipPk.html
index 76fc7db..f29550b 100644
--- src/hg/makeDb/trackDb/human/encTfChipPk.html
+++ src/hg/makeDb/trackDb/human/encTfChipPk.html
@@ -1,44 +1,60 @@
 <h2>Description</h2>
 <p>
 This track represents a comprehensive set of human transcription factor binding sites based on 
 ChIP-seq experiments generated by production groups in the ENCODE Consortium between 
-February 2011 and November 2018. 
-The track presents peak calls (regions of enrichment) 
-generated by the
-the <a target="_blank" href="https://www.encodeproject.org/chip-seq/transcription_factor/">ENCODE Transcription Factor ChIP-seq Processing Pipeline</a>. The related
-<i>Txn Factor ChIP E3</i> tracks 
+February 2011 and November 2018.</>
+<p>
+Transcription factors (TFs) are proteins that bind to DNA and interact with RNA polymerases to
+regulate gene expression.  Some TFs contain a DNA binding domain and can bind directly to 
+specific short DNA sequences ('motifs');
+others bind to DNA indirectly through interactions with TFs containing a DNA binding domain.
+High-throughput antibody capture and sequencing methods (e.g. chromatin immunoprecipitation
+followed by sequencing, or 'ChIP-seq') can be used to identify regions of
+TF binding genome-wide.  These regions are commonly called ChIP-seq peaks.</p>
+
+The related
+<i>Transcription Factor ChIP-seq Clusters</i> tracks 
 (<a target="_blank" href="../cgi-bin/hgTrackUi?db=hg19&g=encRegTfbsClustered">hg19</a>,
 <a target="_blank" href="../cgi-bin/hgTrackUi?db=hg19&g=encRegTfbsClustered">hg38</a>)
-provide a summary views of this data.
+provide summary views of this data.
 </p>  
 <p>
 
 <h2>Display and File Conventions and Configuration</h2>
 <p>
 The display for this track shows site location with the point-source of the peak marked with a 
 colored vertical bar and the level of enrichment at the site indicated by the darkness of the item.
+The subtracks are colored by UCSC ENCODE 2 cell type color conventions on the hg19 assembly, 
+and by similarity of cell types in DNaseI hypersensitivity assays (as in the
+<a target="_blank" href="../cgi-bin/hgTrackUi?db=hg38&g=wgEncodeRegDnaseWig">DNase Signal</a>)
+track in the hg38 assembly.<p>
+
 The display can be filtered to higher valued items, using the 
 <em>Score range:</em> configuration item.
 The score values were computed at UCSC based on signal values assigned by the ENCODE
 pipeline.
 The input signal values were multiplied by a normalization factor calculated as the ratio
 of the maximum score value (1000) to the signal value at 1 standard deviation from the mean,
 with values exceeding 1000 capped at 1000. This has the effect of distributing scores up to 
 mean + 1std across the score range, but assigning all above to the maximum score.
 
 <h2>Methods</h2>
+<p>
+The ChIP-seq peaks in this track were
+generated by the
+the <a target="_blank" href="https://www.encodeproject.org/chip-seq/transcription_factor/">ENCODE Transcription Factor ChIP-seq Processing Pipeline</a>.
 Methods documentation and full metadata for each track can be found at the 
 <a target="_blank" href="https://www.encodeproject.org">ENCODE project portal</a>, using
 The ENCODE file accession (ENCFF*)</em> listed in the track label.
 </p>
 
 <h2>Credits</h2>
 <p>
 Thanks to the ENCODE Consortium, the ENCODE ChIP-seq production laboratories, and the
 ENCODE Data Coordination Center for generating and processing the datasets used here.
 Special thanks to Henry Pratt, Jill Moore, Michael Purcaro, and Zhiping Weng, PI, at the 
 <a target="_blank" href="https://www.umassmed.edu/zlab/">ENCODE Data Analysis Center (ZLab at UMass Medical Center)</a> for providing the peak datasets, metadata, and guidance
 developing this track.</p>
 </p>
 
 <h2>References</h2>