evaluate/document non-gene associated, and non Yali0/Yali1-genome genes

SysBioChalmers / Yarrowia_lipolytica_W29-GEM

Genome-scale model of Yarrowia lipolytica.

http://www.nature.com/articles/npjsba20165

Creative Commons Attribution 4.0 International

8 stars 8 forks source link

evaluate/document non-gene associated, and non Yali0/Yali1-genome genes #10

Open kcorreia opened 6 years ago

kcorreia commented 6 years ago

Any thoughts on what gene catalyzes reaction R_y000208?

It is present in most yeasts but notably absent in the Yarli reference genome. I tried searching with BLASTP/BLASTN but had no luck.

https://www.genome.jp/dbget-bin/get_linkdb?-t+genes+rn:R01954

edit by @edkerk:

[ ] confirm that reactions from SI Table 1 are present in the model
[ ] change rxnNotes for these reactions, to mention that their gene associated is derived from RNAseq data
[ ] decide on how to represent these transcripts as pseudogenes?
[ ] evaluate whether non-gene associated reactions are necessary, and realistic?

edkerk commented 6 years ago

@kcorreia R_y000208 was added during gap-filling, and this gene was indeed not annotated in CLIB122. However, this is a shortcoming of the CLIB122 genome annotation, if you look at SI Table 2 of the npj Syst Biol App paper, you'll see that we did detect transcript that decodes for this gene.

An issue is that the current model has gene annotations referring to CLIB122. Ideally this should be a more generally used strain, such as W29. At least, these 'empty' gene associations should have a note mentioning that mRNA transcripts for this gene have been detected.

I will rename this issue to highlight this problem, and curate the reactions from SI Table 2.

kcorreia commented 6 years ago

Thanks for the quick reply. I had only checked the XML file and hadn't known there was more information in the SI.

edkerk commented 6 years ago

I will keep this open until the model has been curated to contain mentions to the paper in cases where no gene is annotated.