8c2f7318d8d821de9b2a25750586a94ab5e8c1bb lrnassar Fri Nov 15 18:50:19 2024 -0800 Giving the UI link cronjob some love by fixing all the 301 redirects. These are the bulk of the items listed on the cron. No RM. diff --git src/hg/makeDb/trackDb/vistaEnhancersBb.html src/hg/makeDb/trackDb/vistaEnhancersBb.html index 87974e0..d5247f0 100644 --- src/hg/makeDb/trackDb/vistaEnhancersBb.html +++ src/hg/makeDb/trackDb/vistaEnhancersBb.html @@ -1,84 +1,84 @@ <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> +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="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" +<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="http://www.ncbi.nlm.nih.gov/pubmed/14563999" target="_blank" +<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="http://www.ncbi.nlm.nih.gov/pubmed/17086198" target="_blank" +<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="http://www.ncbi.nlm.nih.gov/pubmed/17276707" target="_blank" +<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="http://www.ncbi.nlm.nih.gov/pubmed/18176564" target="_blank" +<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="http://www.ncbi.nlm.nih.gov/pubmed/19212405" target="_blank" +<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="http://www.ncbi.nlm.nih.gov/pubmed/19741700" target="_blank" +<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/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 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> 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>