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Show gene structure diagrams in tooltips #309

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merged 18 commits into from
Aug 4, 2022
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@eweitz eweitz commented Aug 4, 2022

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:

Gene_structure_diagram__Ideogram_2022-08-03.mov

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coveralls commented Aug 4, 2022

Coverage Status

Coverage decreased (-1.6%) to 85.543% when pulling f28256a on gene-structure-tooltips into 2347493 on master.

@eweitz eweitz merged commit 9a5d4cc into master Aug 4, 2022
@eweitz eweitz deleted the gene-structure-tooltips branch August 4, 2022 12:47
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