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eweitz / ideogram

Chromosome visualization for the web
https://eweitz.github.io/ideogram
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Fix CDS size when on same exon as 3'-UTR #322

Closed eweitz closed 2 years ago

eweitz commented 2 years ago

This fixes a bug where some coding sequences (CDS) appeared much too long. This happened when a CDS (yellow part) and 3'-UTR (teal part at right) were on the same exon. It affected mature mRNA diagrams for LDLR, CD44, and many other genes.

Here's how e.g. LDLR looks now:

LDLR_three_prime_UTR_and_CDS_fix__2022-11-05

Confirming the fix by comparing to a reference is difficult. That's because while there are many gene structure diagrams that show mature mRNA for hypothetical genes, there are few concrete examples. One plausible product-level conclusion about this state of the art is that these diagrams in Ideogram are novel (given few concrete examples) and scientifically insightful (given many hypothetical examples).

Fortunately, there is something of a reference concrete example of such diagrams for LDLR:

LDLR_gene_structure_diagram_reference__Gabcova-Balaziova_et_al_2015__Ideogram_2022-11-05

_Source: Figure 1 in Gabcova-Balaziova D, Stanikova D, Vohnout B, Huckova M, Stanik J, Klimes I, Raslova K, Gasperikova D. Molecular-genetic aspects of familial hypercholesterolemia. Endocr Regul. 2015 Jul;49(3):164-81. doi: 10.4149/endo_2015_03164. PMID: 26238499.

Note how the 3'-UTR is roughly the same size as (really, a bit shorter than) the CDS in the reference. It is now the same in the Ideogram mRNA diagram as well. Before, the CDS was about 50% larger than the 3'-UTR. This was clear when comparing against a reference, but basically unnoticeable without one.

coveralls commented 2 years ago

Coverage Status

Coverage increased (+0.02%) to 86.219% when pulling 3a224ddd7787f7629538883cff5e7bbc2dc6192e on fix-exon-utr-overlap into 0937741024a184a3cd2e85216efe831674e488e6 on master.