eweitz / ideogram

Chromosome visualization for the web
https://eweitz.github.io/ideogram
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Show gene structure diagrams in tooltips #309

Closed eweitz closed 2 years ago

eweitz commented 2 years ago

This adds gene structure diagrams to tooltips in the related genes kit.

It highlights exons, introns, and untranslated regions (5'-UTR and 3'-UTR) of the gene's canonical transcript. Seeing how the pre-mRNA transcript is organized is common in genome browsers and can help with gene analysis. (Unlike genome browsers, all transcripts in Ideogram are oriented 5' to 3'; strand information is shown upon hovering over the transcript.) With more development, this UI feature could perhaps show mature mRNA structure and depict conserved domains among paralogs, and annotate them with e.g. topological or functional information.

Gene structure data is fetched from Ensembl genome annotations, using the same GFF file as Ideogram's gene data. Canonical transcripts in the GFF file are extracted by using a list of canonical transcripts IDs from Ensembl BioMart. Ideogram currently only shows gene structure diagrams for human.

Here's how it looks:

https://user-images.githubusercontent.com/1334561/182839470-f27c567c-c571-489a-a66f-45ed1c0dd86a.mov

coveralls commented 2 years ago

Coverage Status

Coverage decreased (-1.6%) to 85.543% when pulling f28256a165481e388d5166a7ffa198767d8e67d5 on gene-structure-tooltips into 2347493b3f441416c3f77095df18c379a2ac01d0 on master.