d90ebafc3574dccc5db20b875c6ebf5cd193e616 gperez2 Thu May 1 16:36:47 2025 -0700 Adding the VISTA Enhancers 2025 update, refs #35531 diff --git src/hg/makeDb/trackDb/human/vistaEnhancersBb.html src/hg/makeDb/trackDb/human/vistaEnhancersBb.html new file mode 100644 index 00000000000..ca90a00db56 --- /dev/null +++ src/hg/makeDb/trackDb/human/vistaEnhancersBb.html @@ -0,0 +1,91 @@ +<H2>Description</H2> + +<p>This track shows potential enhancers whose activity was experimentally validated in transgenic +mice. Most of these noncoding elements were selected for testing based on their extreme conservation +in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. More information +can be found on the <a href="https://enhancer.lbl.gov/" target="_blank">VISTA Enhancer Browser</a> +page. +</p> + +<h2> Display Conventions and Configuration </h2> +<p>Items appearing in <b><font color="#2260f2">blue</font></b> (positive) indicate that a +reproducible pattern was observed in the in vivo enhancer assay under at least one of the +tested conditions. Items appearing in <b><font color="#646464">gray</font></b> (negative) indicate +that NO reproducible pattern was observed in the in vivo enhancer assay under any of the tested +conditions. This does not exclude the possibility that this region is a reproducible enhancer active +under different conditions, for example at an earlier or later timepoint in development.</p> + +<h2>Methods</h2> +<p> Excerpted from the Vista Enhancer <a HREF="https://enhancer.lbl.gov/vista/manual" +TARGET=_BLANK>Mouse Enhancer Screen Handbook and Methods</a> page at the Lawrence Berkeley +National Laboratory (LBNL) website: +<h4>Enhancer Candidate Identification</h4> +<p> Most enhancer candidate sequences are identified by extreme evolutionary sequence conservation or +by ChIP-seq. Detailed information related to enhancer identification by extreme evolutionary +conservation can be found in the following publications: +</p> +<ul> +<li>Pennacchio et al., <a href="https://pubmed.ncbi.nlm.nih.gov/11253049/" target="_blank" +>Genomic strategies to identify mammalian regulatory sequences.</a> Nature Rev Genet 2001</li> +<li>Nobrega et al., <a href="https://pubmed.ncbi.nlm.nih.gov/14563999/" target="_blank" +>Nobrega et al., Scanning human gene deserts for long-range enhancers.</a> Science 2003</li> +<li>Pennacchio et al., <a href="https://pubmed.ncbi.nlm.nih.gov/17086198/" target="_blank" +>In vivo enhancer analysis of human conserved non-coding sequences.</a> Nature 2006</li> +<li>Visel et al., <a href="https://pubmed.ncbi.nlm.nih.gov/17276707/" target="_blank" +>Enhancer identification through comparative genomics.</a> Semin Cell Dev Biol. 2007</li> +<li>Visel et al., <a href="https://pubmed.ncbi.nlm.nih.gov/18176564/" target="_blank" +>Ultraconservation identifies a small subset of extremely constrained developmental enhancers.</a> + Nature Genet 2008</li> +</ul> + +<p>Detailed information related to enhancer identification by ChIP-seq can be found in the +following publications:</p> +<ul> +<li>Visel et al., <a href="https://pubmed.ncbi.nlm.nih.gov/19212405/" target="_blank" +>ChIP-seq accurately predicts tissue-specific activity of enhancers.</a> Nature 2009</li> +<li>Visel et al., <a href="https://pubmed.ncbi.nlm.nih.gov/19741700/" target="_blank" +>Genomic views of distant-acting enhancers.</a> Nature 2009</li> +</ul></p> + +<p>See the Transgenic Mouse Assay section for experimental procedures that were used to perform the +transgenic assays: <a HREF="https://enhancer.lbl.gov/vista/manual" +TARGET=_BLANK>Mouse Enhancer Screen Handbook and Methods</a> + +<p>UCSC converted the +<a href="https://gitlab.com/egsb-mfgl/vista-data/" target="_blank">vista-data</a> bed files for +hg38 and mm10 into bigBed format using the bedToBigBed utility. The data for mm39 was lifted over +from mm10. The data for hg19 was lifted over from hg38.</p> + +<h2>Data Access</h2> +<p> +VISTA Enhancers data can be explored interactively with the +<a href="../cgi-bin/hgTables">Table Browser</a> and cross-referenced with the +<a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For programmatic access, the track can be +accessed using the Genome Browser's <a href="/goldenPath/help/api.html">REST API</a>. ReMap +annotations can be downloaded from the Genome Browser's +<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/vistaEnhancers">download server</a> +as a bigBed file. This compressed binary format can be remotely queried through +command line utilities. Please note that some of the download files can be quite large.</p> + +<h2>Credits</h2> +<p>Thanks to the Lawrence Berkeley National Laboratory for providing this data.</p> + + +<h2>References</h2> +<p> +Kosicki M, Baltoumas FA, Kelman G, Boverhof J, Ong Y, Cook LE, Dickel DE, Pavlopoulos GA, Pennacchio +LA, Visel A. +<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkae940" target="_blank"> +VISTA Enhancer browser: an updated database of tissue-specific developmental enhancers</a>. +<em>Nucleic Acids Res</em>. 2025 Jan 6;53(D1):D324-D330. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39470740" target="_blank">39470740</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11701537/" target="_blank">PMC11701537</a> +</p> +<p> +Visel A, Minovitsky S, Dubchak I, Pennacchio LA. +<a href="https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkl822" target="_blank"> +VISTA Enhancer Browser--a database of tissue-specific human enhancers</a>. +<em>Nucleic Acids Res</em>. 2007 Jan;35(Database issue):D88-92. +PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/17130149" target="_blank">17130149</a>; PMC: <a +href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1716724/" target="_blank">PMC1716724</a> +</p>