5b32ea4a88968fb3a9d1e11d57f1dcbaa642f68e lrnassar Fri Jan 5 14:03:52 2024 -0800 Adding some clarification as to what the offsets mean in the interaction format for the GeneHancer track, refs #24330 diff --git src/hg/makeDb/trackDb/human/geneHancer.html src/hg/makeDb/trackDb/human/geneHancer.html index 15a39f9..c7446c9 100644 --- src/hg/makeDb/trackDb/human/geneHancer.html +++ src/hg/makeDb/trackDb/human/geneHancer.html @@ -18,30 +18,35 @@ <li>Interactions (associations) between regulatory elements and genes</li> <li>Clustered interactions, by gene target or GeneHancer</li> </ul> The full set of elements and interactions is included, along with a highly filtered "double elite" subset. <h2>Display Conventions</h2> <p> Each GeneHancer regulatory element is identified by a GeneHancer id. For example: GH0XJ101383 is located on chromosome X, with starting position of 101,383 kb (GRCh38/hg38 reference). Based on the id, one can obtain full GeneHancer information, as displayed in the Genomics section within the gene-centric web pages of GeneCards. Links to the GeneCards information pages are provided on the track details pages.</p> +<p> +For the interaction tracks (Clusters and Interactions) a slight offset can be noticed between +the line endpoints. This helps to identify the start and end of the feature. In this case, +the higher point is the source (enhancers) and the lower point is the target.</p> + <h3>Regulatory elements</h3> <p> Colors are used to distinguish promoters and enhancers and to indicate the GeneHancer element confidence score:</p> <p> Promoters: <span style="border: 2px inset #000000; background-color:#cc0000;">  </span> High <span style="border: 2px inset #000000; background-color:#ff3333;">  </span> Medium <span style="border: 2px inset #000000; background-color:#ff6666;">  </span> Low </p> <p> Enhancers: <span style="border: 2px inset #000000; background-color:#5F5F5F;">  </span> High <span style="border: 2px inset #000000; background-color:#A0A0A0;">  </span> Medium <span style="border: 2px inset #000000; background-color:#C0C0C0;">  </span> Low </p>