Transcript analysis (Grch37/38) - Log

[zhx828]

biomart mapping file, genes do no have entrez

• grch37 grch37_genes_without_entrez.txt
• grch38 grch38_genes_without_entrez.txt

genes not in cBioPortal

• grch37 grch37_gene_not_in_cbioportal.txt
• grch38 grch38_gene_not_in_cbioportal.txt

hugo symbol does not match with cBioPortal

• grch37 grch37_hugo_symbol_does_not_match_cbioportal.txt
• grch38 grch38_hugo_symbol_does_not_match_cbioportal.txt

Problem(mismatch) transcripts

problem_transcripts.txt

gene protein length check (ones without protein length do not have pfam, vice versa)

• grch37 grch37_info.txt
• grch38 grch38_info.txt

OncoKB issues

Good thing is, for both 37/38, they are using the same transcript. But there are still two issues

• the transcript GN uses vs OncoKB Use are different (I used the msk-transcript column from GN)
• some of the hugo symbols are different grch37_mismatch_gn_oncokb.txt

[inodb]

This is great! Thank you so much!

[inodb]

Thanks again @zhx828 !

A few questions

• What do you mean by:

  ones without protein length do not have pfam, vice versa

• Do we currently have grch38 loaded in the main cBioPortal? I think there is a seed database but im not sure if it's actually loaded. What does it mean exactly when a grch38 gene is not in cBioPortal?

• What are problem mismatch transcripts? They mismatch between grch37 and grch38? Is that based on just the first part of the id? E.g. ENSTx.y so x is the same between grch37 and grch38 or does it include the y version part. Note that the protein length might change when .y changes between grch37 and grch38 (in most cases it does not but occasionally it does)

[zhx828]

• What do you mean by: ones without protein length do not have pfam, vice versa

if you look at the *_info.txt files, the genes that do not have protein length, they do not have pfam data either. So we just need to look at one factor.

• Do we currently have grch38 loaded in the main cBioPortal? I think there is a seed database but im not sure if it's actually loaded. What does it mean exactly when a grch38 gene is not in cBioPortal?

I just pulled the genes from the portal and run through both versions to see whether these entrez genes are in cbioportal. Didn't compare between 37 and 38 though. They might be identical. I think this is mainly for Ramya to finalize the portal gene table.

• What are problem mismatch transcripts? They mismatch between grch37 and grch38? Is that based on just the first part of the id? E.g. ENSTx.y so x is the same between grch37 and grch38 or does it include the y version part. Note that the protein length might change when .y changes between grch37 and grch38 (in most cases it does not but occasionally it does)

I didn't not check y. Only the x to see whether they are the same.

@inodb

[inodb]

Thanks so much @zhx828 !

I didn't not check y. Only the x to see whether they are the same.

I see so there are a few corner cases where even though the id matches the length might not be the same. Yeah it's weird 🙂. So it's good to check if the length matches as well. For starters at least for OncoKB annotated genes

[zhx828]

Thanks so much @zhx828 !

I didn't not check y. Only the x to see whether they are the same.

I see so there are a few corner cases where even though the id matches the length might not be the same. Yeah it's weird 🙂. So it's good to check if the length matches as well. For starters at least for OncoKB annotated genes

Cool, will do. Thanks!

[zhx828]

This is related to https://github.com/genome-nexus/genome-nexus/issues/306