d87e5f63bc000d560c21bca638b6d5f3dee0173d kate Wed Apr 3 12:06:45 2019 -0700 Add scripts and make docs for ENCODE 3 TF binding site tracks. refs #21139 diff --git src/hg/makeDb/trackDb/human/encode3RegTfbsCluster.html src/hg/makeDb/trackDb/human/encode3RegTfbsCluster.html new file mode 100644 index 0000000..2f8ead9 --- /dev/null +++ src/hg/makeDb/trackDb/human/encode3RegTfbsCluster.html @@ -0,0 +1,140 @@ +<h2>Description</h2> +<p> +This track shows 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.</p> +<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> +<p> +ENCODE TF ChIP-seq data were processed using the +<a target="_blank" href="https://www.encodeproject.org/chip-seq/transcription_factor/">ENCODE Transcription Factor ChIP-seq Processing Pipeline</a> 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) are combined here into clusters to produce a +summary display showing occupancy regions for each factor and motif sites +within the regions when identified. +<!-- +# Restore this if we make a track out of underlying peaks + +Additional views of the underlying ChIP-seq data are available from the +<a href="../cgi-bin/hgTrackUi?db=hg19&g=encode3TfbsPk" +target="_blank">ENCODE TFBS</a> track. +--> +<!-- +# Restore this if when we add the motifs +The +<a href="../cgi-bin/hgTrackUi?db=hg19&g=factorbookMotifPos" target=_blank"> +Factorbook Motif</a> track shows the complete set of motif locations +identified in the uniform ENCODE ChIP-seq peaks. +--> +</p> + +<h2>Display Conventions</h2> +<p> +A gray box encloses each peak cluster of transcription factor occupancy, with the +darkness of the box being proportional to the maximum signal strength observed in any cell line +contributing to the cluster. The HGNC gene name for the transcription factor is shown +to the left of each cluster. +<!-- Within a cluster, a green highlight indicates +the highest scoring site of a Factorbook-identified canonical motif for +the corresponding factor. (NOTE: motif highlights are shown +only in browser windows of size 50,000 bp or less, and their display can be suppressed by unchecking +the highlight motifs box on the track configuration page). +Arrows on the highlight designate the matching strand of the motif. +--> +</p> +<p> +The cell lines where signal was detected for the factor are identified by single-letter +abbreviations shown to the right of the cluster. +The darkness of each letter is proportional to the signal strength observed in the cell line. +Abbreviations starting with capital letters designate +<a href="https://www.encodeproject.org/search/?type=Biosample&organism.scientific_name=Homo+sapiens" +target="_blank">ENCODE cell types</a> initially identified for intensive study, +while those starting with lowercase letters designate cell lines added later in the project.</p> +<p> +Click on a peak cluster to see more information about the TF/cell assays contributing to the +cluster and the cell line abbreviation table. +</p> + +<h2>Methods</h2> +<p> +<p> +Peaks of transcription factor occupancy from ENCODE ChIP-seq datasets provided by the +ENCODE Data Analysis Center in November 2018 +were clustered using the UCSC hgBedsToBedExps tool. +Scores were assigned to peaks by multiplying the input signal values by a normalization +factor calculated as the ratio of the maximum score value (1000) to the signal value at one +standard deviation from the mean, with values exceeding 1000 capped at 1000. This has the +effect of distributing scores up to mean plus one 1 standard deviation across the score range, +but assigning all above to the maximum score. +The cluster score is the highest score for any peak contributing to the cluster.</p> +<!-- +<p> +The Factorbook motif discovery and annotation pipeline uses +the MEME-ChIP and FIMO tools from the <a href="http://meme-suite.org/doc/overview.html" +target="_blank">MEME</a> software suite in conjunction with machine learning methods and +manual curation to merge discovered motifs with known motifs reported in +<a target="blank" href="http://jaspar.genereg.net/">Jaspar</a> and +<a href="https://portal.biobase-international.com/build_t/idb/1.0/html/bkldoc/source/bkl/transfac%20suite/transfac/tf_intro.html" +target="_blank">TransFac</a>. +Motif identifications reported in Wang et al. 2012 (below) were supplemented in this track +with more recent data (derived from newer ENCODE datasets - Jan 2011 through Mar 2012 freezes), +provided by the Factorbook team. Motif identifications from all datasets were merged, with +the most significant value (qvalue) reported being picked when motifs were duplicated in +multiple cell lines. The scores for the selected best-scoring motif sites were then transformed +to -log10. +</p> +--> + +<h2>Release Notes</h2> +<p> +Release 5 (2019) of this track comprises 1264 datasets (1256 in hg38), +representing work performed through the 3rd phase of ENCODE. +Release 4 (February 2014) of this track adds display of the Factorbook motifs. +Release 3 (August 2013) added 124 datasets (690 total, vs. 486 in Release 2), +</p> + +<h2>Credits</h2> + +<h2>References</h2> + +<p> +Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, +Alexander R <em>et al</em>. +<a href="https://www.nature.com/articles/nature11245" target="_blank"> +Architecture of the human regulatory network derived from ENCODE data</a>. +<em>Nature</em>. 2012 Sep 6;489(7414):91-100. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22955619" target="_blank">22955619</a> +</p> +<p> +Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y +<em>et al</em>. +<a href="https://genome.cshlp.org/content/22/9/1798.long" target="_blank"> +Sequence features and chromatin structure around the genomic regions bound by 119 human +transcription factors</a>. +<em>Genome Res</em>. 2012 Sep;22(9):1798-812. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/22955990" target="_blank">22955990</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431495/" target="_blank">PMC3431495</a> +</p> +<p> +Wang J, Zhuang J, Iyer S, Lin XY, Greven MC, Kim BH, Moore J, Pierce BG, Dong X, Virgil D <em>et +al</em>. +<a href="https://academic.oup.com/nar/article/41/D1/D171/1069417" target="_blank"> +Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE +consortium</a>. +<em>Nucleic Acids Res</em>. 2013 Jan;41(Database issue):D171-6. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23203885" target="_blank">23203885</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531197/" target="_blank">PMC3531197</a> +</p> + +<h2>Data Release Policy</h2> +<p> +While primary ENCODE data was subject to a restriction period as described in the +<a href="../ENCODE/terms.html" target="_blank"> +ENCODE data release policy</a>, this restriction does not apply to the integrative +analysis results, and all primary data underlying this track have passed the restriction date. +The data in this track are freely available.</p>