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schurerlab / CKI

CKI - Dark Kinase Knowledgebase App
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Pseudogenes #12

Open pnrobinson opened 3 years ago

pnrobinson commented 3 years ago

Four of the gene symbols listed as dark kinase (Tdark) refer to pseudogenes, but this is not reflected in the display in the shiny app.

PRKY https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:9444

GK3P https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:4292

NME2P1 https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:31358

PDPK2P https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:49897

-- Are the gene symbols incorrect or are these entries truly supposed to be pseudogenes?

Rimsk commented 3 years ago

We downloaded all the kinases from IDG/Pharos site and then mapped those with the TCGA data. These genes appeared in TCGA data.

pnrobinson commented 3 years ago

Gene symbols are being changed by the community for consistency and because the literature has used various symbols. Unfortunately this can affect legacy data. In any case, at present, all four of these symbols to not refer to protein-coding genes and so it would be good to update them.