7f892f8fa5f41b18d489cfdbb0255c05b1b3e3f3 jnavarr5 Mon Oct 7 10:55:15 2019 -0700 Updating http to https for hg19, uiLinks cronjob. diff --git src/hg/makeDb/trackDb/human/geneHancer.html src/hg/makeDb/trackDb/human/geneHancer.html index 22997cf..5737ccc 100644 --- src/hg/makeDb/trackDb/human/geneHancer.html +++ src/hg/makeDb/trackDb/human/geneHancer.html @@ -1,20 +1,20 @@ <h2>Description</h2> <p> GeneHancer is a database of human regulatory elements (enhancers and promoters) and their inferred target genes, which is embedded -in <a href="http://www.genecards.org" target="_blank">GeneCards</a>, a human gene +in <a href="https://www.genecards.org/" target="_blank">GeneCards</a>, a human gene compendium. The GeneHancer database was created by integrating >1 million regulatory elements from multiple genome-wide databases. Associations between the regulatory elements and target genes were based on multiple sources of linking molecular data, along with distance, as described in Methods below. </p> <p> The GeneHancer track set contains tracks representing: <ul> <li>Regulatory elements (GeneHancers)</li> <li>Gene transcription start sites</li> <li>Interactions (associations) between regulatory elements and genes</li> <li>Clustered interactions, by gene target or GeneHancer</li> </ul> @@ -71,31 +71,31 @@ (with tall GeneHancer and short TSS's). Clusters composed of interactions with a single gene are colored to correspond to the gene, and those composed of interactions with multiple genes are colored dark gray.</p> <h2>Methods</h2> <p> GeneHancer identifications were created from >1 million regulatory elements obtained from seven genome-wide databases: <ol> <li><a href="https://www.encodeproject.org/" target="_blank">ENCODE project</a> <a href="http://zlab-annotations.umassmed.edu/enhancers/" target="_blank">Z-Lab Enhancer-like regions</a> (version v3)</li> <li><a href="http://ensembl.org/info/genome/funcgen/index.html" target="_blank">Ensembl regulatory build</a> (version 92)</li> <li><a href="http://fantom.gsc.riken.jp/" target="_blank">FANTOM5</a><a href="http://pressto.binf.ku.dk/" target="_blank"> atlas of active enhancers</a></li> -<li><a href="http://enhancer.lbl.gov/" target="_blank">VISTA Enhancer Browser</a></li> +<li><a href="https://enhancer.lbl.gov/" target="_blank">VISTA Enhancer Browser</a></li> <li><a href="http://asntech.org/dbsuper/" target="_blank">dbSUPER super-enhancers</a></li> <li><a href="https://epd.vital-it.ch/EPDnew_database.php" target="_blank">EPDnew promoters</a></li> <li><a href="https://ccg.vital-it.ch/UCNEbase/" target="_blank">UCNEbase ultra-conserved noncoding elements</a></li> </ol> <p> Employing an integration algorithm that removes redundancy, the GeneHancer pipeline identified ˜250k integrated candidate regulatory elements (GeneHancers). Each GeneHancer is assigned an annotation-derived confidence score. The GeneHancers that are derived from more than one information source are defined as "elite" GeneHancers.</p> <p> Gene-GeneHancer associations, and their likelihood-based scores, were generated using information that helps link regulatory elements to genes: <ol> <li>eQTLs (expression quantitative trait loci) from <a href="https://www.gtexportal.org/home/" @@ -105,31 +105,31 @@ <li>Cross-tissue expression correlations between a transcription factor interacting with a GeneHancer and a candidate target gene</li> <li>Distance-based associations, including several approaches: <ol> <li>Nearest neighbors, where each GeneHancer is associated with its two proximal genes</li> <li>Overlaps with the gene territory (intragenic)</li> <li>Proximity to the gene TSS (<2kb)</li> </ol> </ol></p> <p> Associations that are derived from more than one information source are defined as "elite" associations, which leads to the definition of the "double elite" dataset - elite gene associations of elite GeneHancers.</p> <p> More details are provided at the GeneCards -<a href="http://www.genecards.org/Guide/GeneCard/enhancers" target="_blank"> +<a href="https://www.genecards.org/Guide/GeneCard#enhancers" target="_blank"> information page</a>. For a full description of the methods used, refer to the GeneHancer manuscript<sup>1</sup>.</p> <p> Source data for the GeneHancer version 4.8 was downloaded during May 2018.</p> <H2>Data Access</H2> <p> Limited GeneHancer positional data may be explored with the <a href="../cgi-bin/hgTables">Table Browser</a>. The complete data are not found in the UCSC download servers as per the agreement with the Weizmann Institute.</p> <p> GeneHancer is the property of the Weizmann Institute of Science and is not available for download or mirroring by any third party @@ -146,18 +146,18 @@ <p> Contact: <A HREF="mailto:simon. fishilevich@weizmann. ac. il"> simon. fishilevich@weizmann. ac. il</A> <!-- above address is simon.fishilevich at weizmann.ac.il --> <p> Supported in part by a grant from LifeMap Sciences Inc.</p> <h2>References</h2> <p> -Fishilevich S., Nudel R., Rappaport N., Hadar R., Plaschkes I., Iny Stein T., Rosen N., Kohn A., Twik M., Safran M., Lancet D. and Cohen D. <i>GeneHancer: genome-wide integration of enhancers and target genes in GeneCards</i>, Database (Oxford) (2017), doi:10.1093/database/bax028. <a href="https://www.genecards.org/papers/Database-2017-Fishilevich-GH.pdf" target="_blank">[PDF]</a> PMID <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=search&Dopt=b&term=28605766" target="_blank">28605766</a></p> +Fishilevich S., Nudel R., Rappaport N., Hadar R., Plaschkes I., Iny Stein T., Rosen N., Kohn A., Twik M., Safran M., Lancet D. and Cohen D. <i>GeneHancer: genome-wide integration of enhancers and target genes in GeneCards</i>, Database (Oxford) (2017), doi:10.1093/database/bax028. <a href="https://www.genecards.org/papers/Database-2017-Fishilevich-GH.pdf" target="_blank">[PDF]</a> PMID <a href="https://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=28605766&dopt=b" target="_blank">28605766</a></p> <p> -Stelzer G, Rosen R, Plaschkes I, Zimmerman S, Twik M, Fishilevich S, Iny Stein T, Nudel R, Lieder I, Mazor Y, Kaplan S, Dahary, D, Warshawsky D, Guan- Golan Y, Kohn A, Rappaport N, Safran M, and Lancet D. <i>The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analysis</i>, Current Protocols in Bioinformatics (2016), 54:1.30.1-1.30.33. doi: 10.1002/cpbi.5. PMID <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=search&Dopt=b&term=27322403" target="_blank">27322403</a></p> +Stelzer G, Rosen R, Plaschkes I, Zimmerman S, Twik M, Fishilevich S, Iny Stein T, Nudel R, Lieder I, Mazor Y, Kaplan S, Dahary, D, Warshawsky D, Guan- Golan Y, Kohn A, Rappaport N, Safran M, and Lancet D. <i>The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analysis</i>, Current Protocols in Bioinformatics (2016), 54:1.30.1-1.30.33. doi: 10.1002/cpbi.5. PMID <a href="https://www.ncbi.nlm.nih.gov/pubmed?cmd=search&term=27322403&dopt=b" target="_blank">27322403</a></p>