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Enable protein diagrams #334

Merged
merged 26 commits into from
Dec 29, 2022
Merged

Enable protein diagrams #334

merged 26 commits into from
Dec 29, 2022

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eweitz
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@eweitz eweitz commented Dec 29, 2022

This adds protein diagrams to gene leads tooltips. These convey sequence-based, functional information for genes.

Previously, only transcripts / gene structures were shown. These depict the layout of exons, introns, UTRs, and CDS. While useful for comparing exon layout between paralogs, or -- with future enhancements -- how assayed RNA sequence data in a sample relates to reference information, the gene structure diagrams in tooltips were somewhat abstract.

Now, protein diagrams appear below the CDS region of spliced transcript diagrams. Each subpart or segment in a protein diagram represents a feature from InterPro, EBI's protein database. The subparts are protein domains, families, active sites, conserved sites, etc. Hovering over a protein subpart shows its name, which is often its biochemical function.

As an example of such diagrams in the scientific literature, consider these diagrams from Figure 1 in Wu et al. 2011 (PMID 22389749) showing gene (pre-mRNA), mature mRNA, and protein diagrams for the gene AGT:

The serpine domain is now shown for the AGT gene, along with a conserved site in that domain.

Here's how it looks for ACE2 and AGT:

Protein_domain_diagrams__Ideogram_2022-12-28.mov

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Coverage Status

Coverage: 86.68% (+0.1%) from 86.584% when pulling 683f34a on protein-diagrams into 9001144 on master.

@eweitz eweitz merged commit f8ece53 into master Dec 29, 2022
@eweitz eweitz deleted the protein-diagrams branch December 29, 2022 01:06
@eweitz eweitz mentioned this pull request Jan 5, 2023
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2 participants