Pseudogenes

[pnrobinson]

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]

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

[pnrobinson]

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.