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/human/geneHancer.html src/hg/makeDb/trackDb/human/geneHancer.html index c7446c9..eae6d75 100644 --- src/hg/makeDb/trackDb/human/geneHancer.html +++ src/hg/makeDb/trackDb/human/geneHancer.html @@ -72,31 +72,31 @@ associated with it are displayed in a single browser item. The gene TSS and associated GeneHancers are shown as blocks linked together, with the TSS drawn as a "tall" item, and the GeneHancers drawn "short". A user configuration option is provided to change the view to group by GeneHancer (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="https://useast.ensembl.org/info/genome/funcgen/index.html" target="_blank">Ensembl regulatory build</a> (version 92)</li> <li><a href="https://fantom.gsc.riken.jp/" target="_blank">FANTOM5</a><a href="https://pressto.binf.ku.dk/" target="_blank"> atlas of active enhancers</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>