aba55984f35dacd02061eafb2ca9a9784efb8bae kate Thu May 9 16:31:31 2019 -0700 Add/polish track labels and descriptions for ENCODE 3 TF tracks. refs #21139 diff --git src/hg/makeDb/trackDb/human/encTfChipPk.html src/hg/makeDb/trackDb/human/encTfChipPk.html new file mode 100644 index 0000000..76fc7db --- /dev/null +++ src/hg/makeDb/trackDb/human/encTfChipPk.html @@ -0,0 +1,103 @@ +<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 +(<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. +</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 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> +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> + +<p>ENCODE Project Consortium. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/21526222" title="https://www.ncbi.nlm.nih.gov/pubmed/21526222" rel="nofollow" TARGET="_BLANK"> +A user's guide to the encyclopedia of DNA elements (ENCODE)</a>. +<em>PLoS Biol</em>. 2011 Apr;9(4):e1001046. PMID: 21526222; PMCID: PMC3079585 +</p> + +<p>ENCODE Project Consortium. +<a href="https://www.ncbi.nlm.nih.gov/pubmed/22955616" title="https://www.ncbi.nlm.nih.gov/pubmed/22955616" rel="nofollow" TARGET="_BLANK"> +An integrated encyclopedia of DNA elements in the human genome</a>. +<em>Nature</em>. 2012 Sep 6;489(7414):57-74. PMID: 22955616; PMCID: PMC3439153 +</p> +<p> +Sloan CA, Chan ET, Davidson JM, Malladi VS, Strattan JS, Hitz BC, Gabdank I, Narayanan AK, Ho M, Lee +BT <em>et al</em>. +<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkv1160" target="_blank"> +ENCODE data at the ENCODE portal</a>. +<em>Nucleic Acids Res</em>. 2016 Jan 4;44(D1):D726-32. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/26527727" target="_blank">26527727</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702836/" target="_blank">PMC4702836</a> +</p> +<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 Use Policy </H2> +<P> <B>Users may freely download, analyze and publish results based on any ENCODE data without +restrictions.</B> +Researchers using unpublished ENCODE data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional. </> +<p> +<B><I>Users of ENCODE datasets are requested to cite the ENCODE Consortium and ENCODE +production laboratory(s) that generated the datasets used, as described in +<A target="_blank" href="https://www.encodeproject.org/help/citing-encode/">Citing ENCODE</A>.</B></I></p> +