fa272dac584b8d450211f426b50c5e9e6de114c8 mspeir Tue Sep 22 08:40:34 2026 -0700 New FAQ page on regulation and cis-regulatory tracks, refs #24610 Adds FAQ/FAQregulation.html, the page requested in this ticket since 2019: where to find transcription factor binding site data, and how the various cis-regulatory tracks relate to each other. The page is organized around the measured vs predicted distinction, which is what most of the mailing list questions turn on, and then covers which TFBS tracks to use, what to do when a factor is in none of them, loading ENCODE portal data through the portal's own Visualize button, promoters, enhancers, cCREs, restricting to a cell type, and working outward from a gene. It ends with a summary table of 16 tracks. Assembly coverage is given per track and every assembly name is a link to that track's description page on that assembly, since coverage varies a lot (mm39 carries only three of these tracks, and TFBS Conserved was never built for hg38). Also adds the category to FAQ/index.html and a cross-link from the promoter sequence question in FAQ/FAQdownloads.html. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com> diff --git src/hg/htdocs/FAQ/FAQregulation.html src/hg/htdocs/FAQ/FAQregulation.html new file mode 100755 index 00000000000..575f02c1a79 --- /dev/null +++ src/hg/htdocs/FAQ/FAQregulation.html @@ -0,0 +1,521 @@ +<!DOCTYPE html> +<!--#set var="TITLE" value="Genome Browser FAQ" --> +<!--#set var="ROOT" value=".." --> + +<!-- Relative paths to support mirror sites with non-standard GB docs install --> +<!--#include virtual="$ROOT/inc/gbPageStart.html" --> + +<h1>Frequently Asked Questions: Regulation and cis-regulatory tracks</h1> + +<h2>Topics</h2> + +<ul> +<li><a href="#measuredPredicted">What is the difference between measured and predicted binding + sites?</a></li> +<li><a href="#whichTfbs">Which tracks show transcription factor binding sites?</a></li> +<li><a href="#notFound">I cannot find my transcription factor in any track. Where else can I + look?</a></li> +<li><a href="#encodePortal">How do I display ENCODE data that is not already a track?</a></li> +<li><a href="#promoters">Which tracks show promoters?</a></li> +<li><a href="#enhancers">Which tracks show enhancers and other regulatory elements?</a></li> +<li><a href="#ccres">What are cCREs, and which cCRE track should I use?</a></li> +<li><a href="#cellType">How do I restrict a search to one cell type or tissue?</a></li> +<li><a href="#myGene">I have a gene. How do I find the factors that regulate it?</a></li> +<li><a href="#otherGenomes">What is available for assemblies other than human and mouse?</a></li> +<li><a href="#summary">Summary: regulatory tracks by category</a></li> +</ul> +<hr> +<p> +<a href="index.html">Return to FAQ Table of Contents</a></p> + +<p> +The assembly names after each track are links. They open that track's description page on +that assembly, which gives the methods, the data version and the citation. Coverage varies a +lot between assemblies, so check the list before you assume a track exists on the genome you +work with.</p> + +<a name="measuredPredicted"></a> +<h2>The basics</h2> +<p> +The Genome Browser carries a large number of tracks that annotate regulatory regions. Most of +them are in the <em>Regulation</em> track group, which you will find below the browser image on +the <a href="../cgi-bin/hgTracks?db=hg38">main browser page</a>. It is not always obvious which +one you want, because these tracks answer quite different questions even when they all look +like boxes on the screen.</p> + +<h6>What is the difference between measured and predicted binding sites?</h6> +<p> +Nearly every question we get about these tracks comes down to this distinction.</p> +<p> +A <em>measured</em> binding site comes from an experiment, usually ChIP-seq, in which one +protein was pulled down in one cell type under one set of conditions. The site is real in the +sense that the factor was found there in that experiment. It tells you nothing about other cell +types, and the experiment has to have been done for your factor and your tissue for the data to +exist at all.</p> +<p> +A <em>predicted</em> binding site comes from scanning the genome sequence for a motif, a short +pattern that the factor is known to prefer. Predictions exist everywhere in the genome for every +factor with a known motif, regardless of cell type, and most of them are not bound <em>in +vivo</em>. A typical transcription factor motif occurs hundreds of thousands of times in the +human genome, while the factor binds only a few thousand of those positions in any given cell.</p> +<p> +Neither kind is better than the other. To find out where a factor was actually found, use a +measured track. To find out whether some sequence you care about, a variant or a promoter +fragment, could plausibly be bound, use a predicted track. What you cannot do is cite a +prediction as evidence that the factor binds there.</p> + +<a name="whichTfbs"></a> +<h2>Transcription factor binding sites</h2> + +<h6>Which tracks show transcription factor binding sites?</h6> +<p> +For human, three tracks cover most needs. All three are in the <em>Regulation</em> group.</p> +<ul> + <li> + <strong>ReMap ChIP-seq</strong> is the broadest collection of <em>measured</em> sites. ReMap + 2022 integrates the public ChIP-seq experiments for transcriptional regulators from GEO, + ArrayExpress and ENCODE into one atlas, so it covers far more factors and cell types than any + single project. There are three versions: all peaks per experiment, a non-redundant set that + merges similar targets, and cis-regulatory modules. + Available for <a href="../cgi-bin/hgTrackUi?db=hg19&g=ReMap">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=ReMap">hg38</a>, + <a href="../cgi-bin/hgTrackUi?db=mm10&g=ReMap">mm10</a>, + <a href="../cgi-bin/hgTrackUi?db=mm39&g=ReMap">mm39</a> and + <a href="../cgi-bin/hgTrackUi?db=dm6&g=ReMap">dm6</a>.</li> + <li> + <strong>TF ChIP</strong> has the ENCODE 3 transcription factor ChIP-seq peaks, all processed + the same way. That matters if you are comparing experiments instead of looking up one + factor. It covers 340 factors in 129 cell types on hg38, and 338 factors in 130 cell types on + hg19, where the track is named <em>ENCODE 3 TFBS</em> rather than <em>TF ChIP</em>. + Available for <a href="../cgi-bin/hgTrackUi?db=hg19&g=encTfChipPk">hg19</a> and + <a href="../cgi-bin/hgTrackUi?db=hg38&g=encTfChipPk">hg38</a>. An older clustered version of + the + same data is on <a href="../cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3">hg19 as + Txn Factor ChIP</a>.</li> + <li> + <strong>JASPAR Transcription Factors</strong> is the <em>predicted</em> set, made by scanning + the genome with the JASPAR CORE profiles. The current track is JASPAR 2026. Scores are scaled from + 0 to 1000 and reflect how well the sequence matches the profile; the track shows only sites + scoring 400 or above by default, and you can raise that threshold in the track settings. + Available for <a href="../cgi-bin/hgTrackUi?db=hg19&g=jaspar">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=jaspar">hg38</a>, + <a href="../cgi-bin/hgTrackUi?db=mm10&g=jaspar">mm10</a>, + <a href="../cgi-bin/hgTrackUi?db=mm39&g=jaspar">mm39</a>, + <a href="../cgi-bin/hgTrackUi?db=danRer11&g=jaspar">danRer11</a>, + <a href="../cgi-bin/hgTrackUi?db=dm6&g=jaspar">dm6</a>, + <a href="../cgi-bin/hgTrackUi?db=ce11&g=jaspar">ce11</a>, + <a href="../cgi-bin/hgTrackUi?db=galGal6&g=jaspar">galGal6</a>, + <a href="../cgi-bin/hgTrackUi?db=ci3&g=jaspar">ci3</a> and + <a href="../cgi-bin/hgTrackUi?db=sacCer3&g=jaspar">sacCer3</a>.</li> +</ul> +<p> +Two older tracks still come up in questions. <strong>TFBS Conserved</strong> shows predicted +sites that are conserved across human, mouse and rat, on +<a href="../cgi-bin/hgTrackUi?db=hg17&g=tfbsConsSites">hg17</a>, +<a href="../cgi-bin/hgTrackUi?db=hg18&g=tfbsConsSites">hg18</a> and +<a href="../cgi-bin/hgTrackUi?db=hg19&g=tfbsConsSites">hg19</a> only; it has not been updated in +many years and +there is no hg38 version. <strong>ORegAnno</strong> is a curated collection of regulatory +elements taken from the literature, so it is small but every entry has a citation, on +<a href="../cgi-bin/hgTrackUi?db=hg19&g=oreganno">hg19</a>, +<a href="../cgi-bin/hgTrackUi?db=hg38&g=oreganno">hg38</a>, +<a href="../cgi-bin/hgTrackUi?db=mm10&g=oreganno">mm10</a> and +<a href="../cgi-bin/hgTrackUi?db=dm6&g=oreganno">dm6</a>.</p> + +<a name="notFound"></a> +<h6>I cannot find my transcription factor in any track. Where else can I look?</h6> +<p> +First check whether the experiment simply has not been done. ReMap covers the published ChIP-seq +experiments that were available when it was built, so if your factor is absent from ReMap there +may be no public ChIP-seq for it in that organism. The +<a href="https://remap.univ-amu.fr/" target="_blank">ReMap website</a> lets you search by target +and download the peaks per factor, and that is the quickest way to check.</p> +<p> +If the experiment exists but is newer than our tracks, or was done in a cell type we do not +carry, you will need to bring the data in yourself. The usual sources are:</p> +<ul> + <li> + The <a href="https://www.encodeproject.org/" target="_blank">ENCODE portal</a>, for anything + produced by ENCODE. This is the easiest case, because the portal will send the data + straight to our browser for you. See the <a href="#encodePortal">next question</a>.</li> + <li> + <a href="https://www.ncbi.nlm.nih.gov/geo/" target="_blank">GEO</a>, for data submitted + alongside a publication. Many GEO submissions include processed peak files as supplementary + material, usually BED or narrowPeak, which you can load as a + <a href="/goldenPath/help/customTrack.html">custom track</a> after checking that the + coordinates match the assembly you are using.</li> + <li> + <a href="https://www.ncbi.nlm.nih.gov/sra" target="_blank">SRA</a>, for raw sequencing reads. + The Browser cannot display SRA data. Raw reads have to be aligned and peak-called before there + is anything to show, which is a job for a sequence analysis pipeline rather than for us.</li> +</ul> + +<a name="encodePortal"></a> +<h6>How do I display ENCODE data that is not already a track?</h6> +<p> +You do not need to download anything or write a custom track by hand. The ENCODE portal will +open its data in the Genome Browser for you.</p> +<ol> + <li> + Search the <a href="https://www.encodeproject.org/search/?type=Experiment" + target="_blank">ENCODE portal</a> for what you want, narrowing the results with the filters + down the left side. <strong>Assay title</strong>, <strong>Target of assay</strong> (the + factor), <strong>Biosample</strong> (the cell type or tissue) and <strong>Genome + assembly</strong> are the useful ones.</li> + <li> + Click the <strong>Visualize</strong> button above the result list.</li> + <li> + Pick your assembly in the panel that opens, then click <strong>UCSC</strong>.</li> +</ol> +<p> +The Browser opens with every experiment in your filtered result set loaded as a track hub, so +this works just as well for one experiment as for fifty. Restrict the search before you +visualize, since a broad filter can attach a very large number of tracks at once.</p> +<p> +ENCODE also publishes a hub for each individual experiment, which is handy if you are scripting +or want to keep a link in a session. Substitute the accession into this URL:</p> +<pre>https://www.encodeproject.org/experiments/ENCSR000AKO/@@hub/hub.txt</pre> +<p> +and load it from the <a href="../cgi-bin/hgHubConnect#unlistedHubs">My Hubs</a> tab of the Track +Hubs page, or by appending it to a browser URL as +<code>hgTracks?db=hg38&hubUrl=</code> followed by the hub address.</p> +<p> +If you would rather place a single file yourself, note that ENCODE distributes peaks as bigBed +and signal as bigWig, both of which the Browser reads directly. Copy the file URL from the portal; +you do not +need to download the file. Then paste one custom track line at +<a href="../cgi-bin/hgCustom">Add Custom Tracks</a>:</p> +<pre>track type=bigBed name="CTCF K562 peaks" bigDataUrl=https://www.encodeproject.org/files/ENCFF002CEL/@@download/ENCFF002CEL.bigBed</pre> +<p> +The Browser does not download the whole file. bigBed and bigWig are indexed, so it fetches only +the part covering the region you are looking at, which is why a multi-gigabyte signal file opens +in a moment. Full instructions are on the +<a href="/goldenPath/help/customTrack.html">custom tracks help page</a> and the +<a href="/goldenPath/help/hgTrackHubHelp.html">track hub help page</a>.</p> + +<a name="promoters"></a> +<h2>Promoters, enhancers and other elements</h2> + +<h6>Which tracks show promoters?</h6> +<p> +It depends on what you mean by a promoter, and the tracks disagree enough that it matters.</p> +<ul> + <li> + <strong>EPDnew Promoters</strong> has experimentally defined promoters, each with a single, + precisely mapped transcription start site. Use it when you need a defined, citable promoter + region and not an approximation. On hg38 there is a companion + set for non-coding RNA promoters. + Available for <a href="../cgi-bin/hgTrackUi?db=hg19&g=epdNew">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=epdNew">hg38</a> and + <a href="../cgi-bin/hgTrackUi?db=mm10&g=epdNew">mm10</a>.</li> + <li> + <strong>FANTOM5</strong> maps transcription start sites by CAGE and reports how much each one + is used across a large panel of tissues and cell types. Use it when you want to know which + start site is active in which tissue. + Available for <a href="../cgi-bin/hgTrackUi?db=hg19&g=fantom5">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=fantom5">hg38</a> and + <a href="../cgi-bin/hgTrackUi?db=mm10&g=fantom5">mm10</a>, and for a few other + genomes including chicken, dog, rat and rhesus.</li> + <li> + The promoter-like cCREs in the <a href="#ccres">ENCODE cCRE tracks</a> are a genome-wide + classification built from chromatin signal, so they are more inclusive and less precise than + EPDnew.</li> + <li> + If all you need is a fixed window upstream of a gene, do not use a promoter track at all. The + Table Browser can return the upstream sequence for any gene track, and our download server + carries prepackaged 1000, 2000 and 5000 bp upstream sequence files for RefSeq genes. See + <a href="FAQdownloads.html#download18">Obtaining promoter sequence</a>.</li> +</ul> + +<a name="enhancers"></a> +<h6>Which tracks show enhancers and other regulatory elements?</h6> +<ul> + <li> + <strong>GeneHancer</strong> is the track most users want when they ask about enhancers. It + marks the elements and also links them to their predicted target genes, drawn as + interactions. + Available for <a href="../cgi-bin/hgTrackUi?db=hg19&g=geneHancer">hg19</a> and + <a href="../cgi-bin/hgTrackUi?db=hg38&g=geneHancer">hg38</a>.</li> + <li> + <strong>VISTA Enhancers</strong> has elements that were tested one at a time in transgenic + mouse assays, with the resulting expression pattern recorded. It is the smallest of these + sets and the best validated. + Available for <a href="../cgi-bin/hgTrackUi?db=hg19&g=vistaEnhancersBb">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=vistaEnhancersBb">hg38</a>, + <a href="../cgi-bin/hgTrackUi?db=mm10&g=vistaEnhancersBb">mm10</a> + and <a href="../cgi-bin/hgTrackUi?db=mm39&g=vistaEnhancersBb">mm39</a>.</li> + <li> + <strong>RefSeq Functional Elements</strong> is NCBI's curated set of experimentally + characterized non-coding elements. + Available for <a href="../cgi-bin/hgTrackUi?db=hg38&g=refSeqFuncElems">hg38</a> and + <a href="../cgi-bin/hgTrackUi?db=mm10&g=refSeqFuncElems">mm10</a>.</li> + <li> + <strong>MPRAs</strong> is a collection of massively parallel reporter assay results. These + measure regulatory activity for many sequences at once. + Available for <a href="../cgi-bin/hgTrackUi?db=hg38&g=mpra">hg38</a>.</li> +</ul> +<p> +For the chromatin evidence behind the called elements, see +<a href="../cgi-bin/hgTrackUi?db=hg38&g=wgEncodeReg4">ENCODE4 Regulation</a> on hg38, which +carries DNase, ATAC-seq, histone +modification and CTCF signal organized by tissue, and the older ENCODE3 Regulation container on +<a href="../cgi-bin/hgTrackUi?db=hg19&g=wgEncodeReg">hg19</a> and +<a href="../cgi-bin/hgTrackUi?db=hg38&g=wgEncodeReg">hg38</a>.</p> + +<a name="ccres"></a> +<h6>What are cCREs, and which cCRE track should I use?</h6> +<p> +A candidate cis-regulatory element, or cCRE, is a region that looks regulatory in chromatin +data. Nobody has shown that it regulates anything. ENCODE built the +Registry of cCREs by combining DNase accessibility with histone modification and CTCF signal +across many biosamples, then classifying each region as promoter-like, enhancer-like, CTCF-only +and so on. The word <em>candidate</em> is doing real work here: these are regions worth testing, +not confirmed regulatory elements.</p> +<p> +The <a href="../cgi-bin/hgTrackUi?db=hg38&g=cCREs">ENCODE cCREs</a> container on hg38 holds +several versions. The <strong>ENCODE4 +cCREs</strong> registry is the current one and should be your default. The <strong>ENCODE4 Core +Collection</strong> is a smaller, higher-confidence subset. <strong>ENCODE3 cCREs</strong> is the +earlier release, kept because a great many published analyses used it and coordinates need to +stay reproducible. The container also carries per-biosample subtracks, which is how you restrict +the classification to one cell type. <a href="../cgi-bin/hgTrackUi?db=mm10&g=cCREs">Mouse +mm10</a> carries the same three versions.</p> + +<a name="cellType"></a> +<h2>Working with the data</h2> + +<h6>How do I restrict a search to one cell type or tissue?</h6> +<p> +Most of the large regulatory tracks are composites or superTracks holding many subtracks, one +per cell type or experiment, and they arrive with only a summary view turned on. Click the track +name to open its configuration page, where you will find the list of subtracks and, on the +bigger tracks, filters. ReMap, for instance, lets you filter by transcription factor directly in +the track settings, so you can show one factor across all its experiments.</p> +<p> +To find a track rather than configure one, the +<a href="../cgi-bin/hgTracks?hgt_tSearch=track+search">Track Search</a> page searches track +names and descriptions across the whole assembly, which is usually faster than reading through +the track groups.</p> + +<a name="myGene"></a> +<h6>I have a gene. How do I find the factors that regulate it?</h6> +<p> +No single track answers this, so you have to work outward from the gene.</p> +<ol> + <li> + Navigate to the gene and zoom out far enough to include the surrounding non-coding sequence. + Regulatory elements are often tens or hundreds of kilobases away, and the nearest gene to an + element is frequently not its target.</li> + <li> + Turn on GeneHancer. Its interaction arcs will show which elements have been linked to your + gene, including distant ones, which narrows the search from the whole neighborhood to a + handful of regions.</li> + <li> + Turn on ReMap or TF ChIP and look at which factors have peaks in those regions. This gives you + factors that were measured at that position in some cell type.</li> + <li> + Check whether any of those cell types are relevant to your biology. A peak in K562 says little + about neurons.</li> + <li> + If you need candidates in a cell type nobody has assayed, fall back to JASPAR predictions + within the GeneHancer elements, and treat the result as hypotheses to test.</li> +</ol> +<p> +To do this systematically, the +<a href="../cgi-bin/hgIntegrator">Data Integrator</a> will intersect two or more tracks and +return a table, and the <a href="../cgi-bin/hgTables">Table Browser</a> will do the same for a +region or for a list of genes.</p> + +<a name="otherGenomes"></a> +<h6>What is available for assemblies other than human and mouse?</h6> +<p> +Considerably less, and this is a matter of what data exists rather than what we have loaded. The +large regulatory resources were built for human first and mouse second. JASPAR predictions are +the most widely available, since they only require the genome sequence and a motif, and are +present for zebrafish, fly, worm, chicken, sea squirt and yeast in addition to human and mouse. +ReMap and ORegAnno cover fly. Most of the remaining tracks described on this page are human and +mouse only.</p> +<p> +Coverage also differs between assemblies of the same organism. On mouse, mm10 carries most of +the regulatory tracks while mm39 has only JASPAR, ReMap and VISTA, because several of the source +projects have not released mm39 versions. If a track you need is on mm10 but not mm39, the +<a href="../cgi-bin/hgLiftOver">LiftOver</a> tool can convert coordinates between the two, +though you should check the result. Human has the same problem on a smaller scale: a few of +these tracks are still hg19 only, and TFBS Conserved was never rebuilt for hg38.</p> +<p> +For assemblies not hosted at UCSC, or for tracks we do not carry, check the +<a href="../cgi-bin/hgHubConnect">public hubs</a> list, where other groups publish data through +our browser.</p> + +<a name="summary"></a> +<h2>Summary: regulatory tracks by category</h2> +<p> +Each assembly name below links to that track's description page on that assembly. A few tracks +appear on additional genomes not listed here; use +<a href="../cgi-bin/hgTracks?hgt_tSearch=track+search">Track Search</a> to check a genome that is +not shown.</p> +<table class="stdTbl"> + <thead style="text-align: left"> + <tr> + <th>Track</th> + <th>What it is</th> + <th>Measured or predicted</th> + <th>Assemblies</th> + </tr> + </thead> + <tbody> + <tr> + <td colspan="4"><em>Transcription factor binding</em></td> + </tr> + <tr> + <td>ReMap ChIP-seq</td> + <td>Public ChIP-seq for transcriptional regulators, integrated</td> + <td>Measured</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg19&g=ReMap">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=ReMap">hg38</a>, + <a href="../cgi-bin/hgTrackUi?db=mm10&g=ReMap">mm10</a>, + <a href="../cgi-bin/hgTrackUi?db=mm39&g=ReMap">mm39</a>, + <a href="../cgi-bin/hgTrackUi?db=dm6&g=ReMap">dm6</a></td> + </tr> + <tr> + <td>TF ChIP (ENCODE 3 TFBS on hg19)</td> + <td>ENCODE 3 TF ChIP-seq peaks, around 340 factors in about 130 cell types</td> + <td>Measured</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg19&g=encTfChipPk">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=encTfChipPk">hg38</a></td> + </tr> + <tr> + <td>JASPAR Transcription Factors</td> + <td>Motif matches from the JASPAR CORE collection</td> + <td>Predicted</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg19&g=jaspar">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=jaspar">hg38</a>, + <a href="../cgi-bin/hgTrackUi?db=mm10&g=jaspar">mm10</a>, + <a href="../cgi-bin/hgTrackUi?db=mm39&g=jaspar">mm39</a>, + <a href="../cgi-bin/hgTrackUi?db=danRer11&g=jaspar">danRer11</a>, + <a href="../cgi-bin/hgTrackUi?db=dm6&g=jaspar">dm6</a>, + <a href="../cgi-bin/hgTrackUi?db=ce11&g=jaspar">ce11</a>, + <a href="../cgi-bin/hgTrackUi?db=galGal6&g=jaspar">galGal6</a>, + <a href="../cgi-bin/hgTrackUi?db=ci3&g=jaspar">ci3</a>, + <a href="../cgi-bin/hgTrackUi?db=sacCer3&g=jaspar">sacCer3</a></td> + </tr> + <tr> + <td>TFBS Conserved</td> + <td>Conserved motif matches; not updated recently, no hg38 version</td> + <td>Predicted</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg17&g=tfbsConsSites">hg17</a>, + <a href="../cgi-bin/hgTrackUi?db=hg18&g=tfbsConsSites">hg18</a>, + <a href="../cgi-bin/hgTrackUi?db=hg19&g=tfbsConsSites">hg19</a></td> + </tr> + <tr> + <td>ORegAnno</td> + <td>Regulatory elements curated from the literature</td> + <td>Measured, curated</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg19&g=oreganno">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=oreganno">hg38</a>, + <a href="../cgi-bin/hgTrackUi?db=mm10&g=oreganno">mm10</a>, + <a href="../cgi-bin/hgTrackUi?db=dm6&g=oreganno">dm6</a></td> + </tr> + <tr> + <td colspan="4"><em>Promoters and transcription start sites</em></td> + </tr> + <tr> + <td>EPDnew Promoters</td> + <td>Experimentally defined promoters with mapped start sites</td> + <td>Measured</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg19&g=epdNew">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=epdNew">hg38</a>, + <a href="../cgi-bin/hgTrackUi?db=mm10&g=epdNew">mm10</a></td> + </tr> + <tr> + <td>FANTOM5</td> + <td>CAGE transcription start sites and their usage per tissue</td> + <td>Measured</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg19&g=fantom5">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=fantom5">hg38</a>, + <a href="../cgi-bin/hgTrackUi?db=mm10&g=fantom5">mm10</a></td> + </tr> + <tr> + <td colspan="4"><em>Enhancers and candidate elements</em></td> + </tr> + <tr> + <td>GeneHancer</td> + <td>Regulatory elements linked to predicted target genes</td> + <td>Mixed, with predicted targets</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg19&g=geneHancer">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=geneHancer">hg38</a></td> + </tr> + <tr> + <td>VISTA Enhancers</td> + <td>Elements tested individually in transgenic mouse assays</td> + <td>Measured, validated</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg19&g=vistaEnhancersBb">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=vistaEnhancersBb">hg38</a>, + <a href="../cgi-bin/hgTrackUi?db=mm10&g=vistaEnhancersBb">mm10</a>, + <a href="../cgi-bin/hgTrackUi?db=mm39&g=vistaEnhancersBb">mm39</a></td> + </tr> + <tr> + <td>ENCODE cCREs</td> + <td>Candidate elements classified from chromatin signal</td> + <td>Predicted from measured signal</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg38&g=cCREs">hg38</a>, + <a href="../cgi-bin/hgTrackUi?db=mm10&g=cCREs">mm10</a></td> + </tr> + <tr> + <td>RefSeq Functional Elements</td> + <td>NCBI curated non-coding functional elements</td> + <td>Measured, curated</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg38&g=refSeqFuncElems">hg38</a>, + <a href="../cgi-bin/hgTrackUi?db=mm10&g=refSeqFuncElems">mm10</a></td> + </tr> + <tr> + <td>MPRAs</td> + <td>Massively parallel reporter assay activity</td> + <td>Measured</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg38&g=mpra">hg38</a></td> + </tr> + <tr> + <td colspan="4"><em>Chromatin and expression context</em></td> + </tr> + <tr> + <td>ENCODE4 Regulation</td> + <td>DNase, ATAC, histone marks and CTCF by tissue</td> + <td>Measured</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg38&g=wgEncodeReg4">hg38</a></td> + </tr> + <tr> + <td>ENCODE3 Regulation</td> + <td>DNase, histone marks and transcription signal</td> + <td>Measured</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg19&g=wgEncodeReg">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=wgEncodeReg">hg38</a></td> + </tr> + <tr> + <td>Single-cell ATAC-seq</td> + <td>Accessibility peaks and signal from Cell Browser datasets</td> + <td>Measured</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg38&g=singleCellSignalsPeaks">hg38</a>, + <a href="../cgi-bin/hgTrackUi?db=mm10&g=singleCellSignalsPeaks">mm10</a></td> + </tr> + <tr> + <td>GTEx Gene</td> + <td>Gene expression across 53 tissues</td> + <td>Measured</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg19&g=gtexGene">hg19</a>, + <a href="../cgi-bin/hgTrackUi?db=hg38&g=gtexGene">hg38</a></td> + </tr> + <tr> + <td>GTEx cis-eQTLs</td> + <td>Variants associated with expression of nearby genes</td> + <td>Measured</td> + <td><a href="../cgi-bin/hgTrackUi?db=hg38&g=gtexEqtlHighConf">hg38</a></td> + </tr> + </tbody> +</table> + +<p> +For the full set of tracks on any assembly, open the <em>Regulation</em> group on the +<a href="../cgi-bin/hgTracks?db=hg38">browser page</a>, or use +<a href="../cgi-bin/hgTracks?hgt_tSearch=track+search">Track Search</a>.</p> + +<!--#include virtual="$ROOT/inc/gbPageEnd.html" -->