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.

Methods

GeneHancer identifications were created from >1 million regulatory elements obtained from seven genome-wide databases:

  1. ENCODE project Z-Lab Enhancer-like regions (version v3)
    2. -
  2. Ensembl regulatory build (version 92)
    3. +
  3. Ensembl regulatory build (version 92)
  4. FANTOM5 atlas of active enhancers
  5. VISTA Enhancer Browser
  6. dbSUPER super-enhancers
  7. EPDnew promoters
  8. UCNEbase ultra-conserved noncoding elements

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.