Ortholog Table for Cross-Species Comparisons

[mhwadsworth91]

Dear Developer,

Thank you for the comprehensive vignette; I've enjoyed learning this method, especially for cross-species analyses. Specifically, I am curious how you created the ortholog table. Would it be possible to post this method in the SCN repository (if the code exists)? If not, no worries. My motivation for asking primarily comes from the desire to quickly and efficiently create ortholog tables for (1) multiple species or (2) when new versions of references become available.

Thank you for your time.

[pcahan1]

Hi,

Thank you for your interest in SCN.

We used https://www.genenames.org/tools/hcop/ to generate an initial list of orthologs. Then we generated a final ortholog table by finding pairs in which expression correlation across tissues was maximal. I can post that code to the repo later. The tissues expression for mouse and human was derived from bulk RNAseq.

[mhwadsworth91]

Hello,

Thank you for this information and for uploading that code; I really appreciate your time.

[mhwadsworth91]

Dear Developer,

I wanted to follow-up on this issue and see if there's any update on posting the code to the repo? I think this would be very valuable for users.

Thank you for your time.

[mhwadsworth91]

Dear Developer,

I hope this finds you well. Just following up on this.

Thank you for your time.