859df2c7c8948da00a2305e90fafe00016032ca7 gperez2 Thu May 8 12:41:02 2025 -0700 code review edits, refs #35693 diff --git src/hg/makeDb/trackDb/human/vistaEnhancersBb.html src/hg/makeDb/trackDb/human/vistaEnhancersBb.html index ca90a00db56..d85ecced2aa 100644 --- src/hg/makeDb/trackDb/human/vistaEnhancersBb.html +++ src/hg/makeDb/trackDb/human/vistaEnhancersBb.html @@ -1,91 +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 +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> +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>