2f68ddece42ca7ef91bcaa53dfc9b6940b0ef1e3 gperez2 Wed Sep 27 13:56:11 2023 -0700 Making VISTA Enhancers into native track, refs #16044 diff --git src/hg/makeDb/trackDb/vistaEnhancersBb.html src/hg/makeDb/trackDb/vistaEnhancersBb.html new file mode 100644 index 0000000..be77780 --- /dev/null +++ src/hg/makeDb/trackDb/vistaEnhancersBb.html @@ -0,0 +1,85 @@ +<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="http://enhancer.lbl.gov" target="_blank">VISTA Enhancer Browser</a> +page. +</p> + +<h2> Display Conventions and Configuration </h2> +<p> Items appearing in <b><font color="red">red</font></b> (positive) indicate that a reproducible +pattern was observed in the in vivo enhancer assay. Items appearing in +<b><font color="blue">blue</font></b> (negative) indicate that NO reproducible pattern was observed +in the in vivo enhancer assay. Note that this annotation refers only to the single developmental +timepoint that was tested in this screen (e11.5) and does not exclude the possibility that this +region is a reproducible enhancer active at earlier or later timepoints in development. +</p> + +<h2>Methods</h2> +<p> Excerpted from the Vista Enhancer <a HREF="https://enhancer.lbl.gov/aboutproject_n.html" +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="http://www.ncbi.nlm.nih.gov/pubmed/11253049" target="_blank" +>Genomic strategies to identify mammalian regulatory sequences.</a> Nature Rev Genet 2001</li> +<li>Nobrega et al., <a href="http://www.ncbi.nlm.nih.gov/pubmed/14563999" target="_blank" +>Nobrega et al., Scanning human gene deserts for long-range enhancers.</a> Science 2003</li> +<li>Pennacchio et al., <a href="http://www.ncbi.nlm.nih.gov/pubmed/17086198" target="_blank" +>In vivo enhancer analysis of human conserved non-coding sequences.</a> Nature 2006</li> +<li>Visel et al., <a href="http://www.ncbi.nlm.nih.gov/pubmed/17276707" target="_blank" +>Enhancer identification through comparative genomics.</a> Semin Cell Dev Biol. 2007</li> +<li>Visel et al., <a href="http://www.ncbi.nlm.nih.gov/pubmed/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="http://www.ncbi.nlm.nih.gov/pubmed/19212405" target="_blank" +>ChIP-seq accurately predicts tissue-specific activity of enhancers.</a> Nature 2009</li> +<li>Visel et al., <a href="http://www.ncbi.nlm.nih.gov/pubmed/19741700" target="_blank" +>Genomic views of distant-acting enhancers.</a> Nature 20099</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/aboutproject_n.html" +TARGET=_BLANK>Mouse Enhancer Screen Handbook and Methods</a> + +<p>UCSC converted the +<a href="https://enhancer.lbl.gov/cgi-bin/imagedb3.pl?show=1;page=1;search.form=no;page_size=20000;action=search;form=search;search.result=yes;search.sequence=1" +target="_blank">Experimental Data</a> for hg19 and mm9 into bigBed format using the bedToBigBed +utility. The data for hg38 was lifted over from hg19. The data for mm10 and mm39 were lifted over +from mm9.</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 +<a href="https://hgdownload.soe.ucsc.edu/gbdb/$db/vistaEnhancers">Genome Browser's 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> +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>