9687a91909838021ee4ca314e2a29c0cccd845c8 mspeir Sat Sep 26 16:32:35 2026 -0700 commenting out the section about loading ENCODE files as CTs, refs #24610 diff --git src/hg/htdocs/FAQ/FAQregulation.html src/hg/htdocs/FAQ/FAQregulation.html index 22999c560f5..debed8a8caa 100755 --- src/hg/htdocs/FAQ/FAQregulation.html +++ src/hg/htdocs/FAQ/FAQregulation.html @@ -1,575 +1,576 @@ <!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="#variantEffect">I have a variant, not a region. What does it do to regulation?</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">main browser page</a>.</p> <h6>What is the difference between measured and predicted binding sites?</h6> <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 <a href="/goldenPath/help/hgRegMotifHelp.html">motif</a>, the sequence theme a given factor prefers, usually stored as a position weight matrix and not a single spelling. 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, <em>Txn Factor ChIP</em>, is on <a href="../cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegTfbsClusteredV3">hg19</a>.</li> <li> <strong>JASPAR Transcription Factors</strong> is the <em>predicted</em> set, made by scanning the genome with the JASPAR CORE profiles. 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. Clicking a site shows the <a href="/goldenPath/help/hgRegMotifHelp.html">motif display</a>, with the sequence logo and the matrix behind the score. The track holds several JASPAR releases as separate subtracks, so check which one you have turned on before you quote a version. JASPAR 2026 is on <a href="../cgi-bin/hgTrackUi?db=hg38&g=jaspar">hg38</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=galGal6&g=jaspar">galGal6</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=ci3&g=jaspar">ci3</a> and <a href="../cgi-bin/hgTrackUi?db=sacCer3&g=jaspar">sacCer3</a>. On <a href="../cgi-bin/hgTrackUi?db=hg19&g=jaspar">hg19</a> and <a href="../cgi-bin/hgTrackUi?db=mm10&g=jaspar">mm10</a> the newest release is JASPAR 2024.</li> </ul> <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 load the data yourself as a custom track. 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> 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, which measure regulatory activity for many sequences at once. The MPRA Base half holds 40,938 tested elements; the MPRAVarDB half holds tested variants and is covered under <a href="#variantEffect">variant effects</a> below. 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 <strong>ENCODE4 Regulation</strong>, which carries DNase, ATAC-seq, histone modification and CTCF signal organized by tissue, on <a href="../cgi-bin/hgTrackUi?db=hg38&g=wgEncodeReg4">hg38</a> and <a href="../cgi-bin/hgTrackUi?db=mm10&g=encode4Reg">mm10</a>. This replaced <strong>ENCODE3 Regulation</strong> as the default in July 2026; ENCODE3 is kept for archival use and is still 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.</p> <p> The <strong>ENCODE cCREs</strong> container on <a href="../cgi-bin/hgTrackUi?db=hg38&g=cCREs">hg38</a> holds several versions. The <strong>ENCODE4 cCREs</strong> registry became the default in July 2026 and is the one to use: 2.3 million human and 927,000 mouse elements. The <strong>ENCODE4 Core Collection</strong> is a smaller, higher-confidence subset, covering the 170 human and 18 mouse biosamples that were profiled with all four core assays. <strong>ENCODE3 cCREs</strong> is the earlier release, kept for archival use 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. Mouse <a href="../cgi-bin/hgTrackUi?db=mm10&g=cCREs">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 collections holding many separate tracks, 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 and, on the bigger collections, 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> The largest collections use a different configuration page. Where there are hundreds or thousands of individual experiments, as in the per-experiment tracks of <strong>ENCODE4 Regulation</strong> on <a href="../cgi-bin/hgTrackUi?db=hg38&g=wgEncodeReg4">hg38</a>, the page shows facets down the left side and a paginated table on the right: tick the tissue, assay or biosample you want and the table narrows to the matching experiments. This is usually a faster way to reach one cell type than reading a long list.</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="variantEffect"></a> <h6>I have a variant, not a region. What does it do to regulation?</h6> <p> This is a different question from the rest of this page. Everything above annotates regions and tells you what is where; the tracks here take one base change and tell you what it does. The same measured and predicted distinction applies, so start with the one track that is measured.</p> <p> <strong>MPRAVarDB</strong> holds 239,028 variants that were put through a reporter assay and scored for allelic effect, drawn from 18 MPRA studies covering more than 30 cell lines and more than 30 diseases or traits. The variants come from GWAS and eQTL fine-mapping, from saturation mutagenesis of 20 disease-associated regulatory elements, and from smaller focused screens, so the coverage is concentrated on loci people have already had reason to care about. Items are colored by significance, dark red for FDR below 0.05. If your variant is in here, you have an experimental answer and not a guess. It lives in the <strong>MPRAs</strong> collection, alongside MPRA Base, which tests whole elements. Available for <a href="../cgi-bin/hgTrackUi?db=hg38&g=mpraVarDb">hg38</a>.</p> <p> Most variants will not be in it, since 239,028 tested positions is a very small part of the genome. Two prediction tracks fill the gap by scoring every possible substitution, and neither is in the <em>Regulation</em> group: look under <em>Phenotype and Disease Associations</em>, in the <strong>Deleteriousness Predictions</strong> collection on <a href="../cgi-bin/hgTrackUi?db=hg38&g=predictionScoresSuper">hg38</a>.</p> <ul> <li> <strong>AlphaGenome</strong> gives the AlphaGenome Variant Impact score from Google DeepMind, which folds together predicted effects on expression, splicing, chromatin accessibility and transcription factor binding across hundreds of cell types, plus AlphaMissense for changes that alter protein. It is precomputed for every possible single-base substitution in the genome, about 8.8 billion of them, with one track per alternate allele. Scores are PHRED scaled, so 10 marks the top 10 percent of substitutions genome-wide, 20 the top 1 percent and 30 the top 0.1 percent. Unusually for a score of this kind it covers non-coding bases as well as coding ones, which is what makes it useful here. Available for <a href="../cgi-bin/hgTrackUi?db=hg38&g=alphaGenome">hg38</a>.</li> <li> <strong>PromoterAI</strong>, from Illumina, scores every possible single-base substitution in proximal promoter regions. Narrower than AlphaGenome and aimed squarely at promoter variants. Available for <a href="../cgi-bin/hgTrackUi?db=hg38&g=promoterAi">hg38</a>.</li> </ul> <p> A high score from either says a model thinks the change is disruptive, not that anyone has measured it. Where a variant appears in both MPRAVarDB and a prediction track, the measurement is the better evidence.</p> <a name="otherGenomes"></a> <h6>What is available for assemblies other than human and mouse?</h6> <p> Much less. The limit is usually the data itself: these resources were built for human first, and most never went further than mouse. JASPAR is the main exception, since it needs only the genome sequence and a motif, so it covers zebrafish, fly, worm, chicken, sea squirt and yeast as well. ReMap also covers fly. Everything else described on this page is human and mouse only.</p> <p> Mouse is split awkwardly between its own assemblies. mm10 carries most of these tracks and mm39 has only JASPAR, ReMap and VISTA, because several of the source projects never released mm39 versions. If you need something that is on mm10 but not mm39, <a href="../cgi-bin/hgLiftOver">LiftOver</a> will convert the coordinates, though check the result before trusting it. Human has a milder version of the same problem: a few tracks, such as the older clustered Txn Factor ChIP, are still hg19 only.</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; several releases as subtracks</td> <td>Predicted</td> <td>JASPAR 2026 on <a href="../cgi-bin/hgTrackUi?db=hg38&g=jaspar">hg38</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=galGal6&g=jaspar">galGal6</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=ci3&g=jaspar">ci3</a>, <a href="../cgi-bin/hgTrackUi?db=sacCer3&g=jaspar">sacCer3</a>; up to JASPAR 2024 on <a href="../cgi-bin/hgTrackUi?db=hg19&g=jaspar">hg19</a> and <a href="../cgi-bin/hgTrackUi?db=mm10&g=jaspar">mm10</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; ENCODE4 is the default</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 (MPRA Base)</td> <td>Reporter assay activity for 40,938 tested regulatory elements</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; the current default</td> <td>Measured</td> <td><a href="../cgi-bin/hgTrackUi?db=hg38&g=wgEncodeReg4">hg38</a>, <a href="../cgi-bin/hgTrackUi?db=mm10&g=encode4Reg">mm10</a></td> </tr> <tr> <td>ENCODE3 Regulation</td> <td>DNase, histone marks and transcription signal; archival, replaced by ENCODE4</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> <tr> <td colspan="4"><em>Effect of a single variant</em></td> </tr> <tr> <td>MPRAVarDB</td> <td>239,028 variants tested for allelic effect in reporter assays</td> <td>Measured</td> <td><a href="../cgi-bin/hgTrackUi?db=hg38&g=mpraVarDb">hg38</a></td> </tr> <tr> <td>AlphaGenome</td> <td>Variant Impact score for every single-base substitution, coding and non-coding; under Phenotype and Disease Associations</td> <td>Predicted</td> <td><a href="../cgi-bin/hgTrackUi?db=hg38&g=alphaGenome">hg38</a></td> </tr> <tr> <td>PromoterAI</td> <td>Score for every single-base substitution in proximal promoters; under Phenotype and Disease Associations</td> <td>Predicted</td> <td><a href="../cgi-bin/hgTrackUi?db=hg38&g=promoterAi">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">browser page</a>, or use <a href="../cgi-bin/hgTracks?hgt_tSearch=track+search">Track Search</a>.</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->