Updated analysis: Update kinase reference gene list for fusion filtering

[kgaonkar6]

What analysis module should be updated and why?

Kinase reference list from http://kinase.com/human/kinome/tables/ needs to be updated.

What changes need to be made? Please provide enough detail for another participant to make the update.

This will be updated using Kinase domain location form pfam (http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/ucscGenePfam.txt.gz) overlapped with gene locations to identify kinase proteins.

Genes with the following domain names will be considered Kinase genes and added
names(table(pfam[grep(“kinase”,pfam$X4),“X4"]))
[1] “AA_kinase” “Alpha_kinase” “APS_kinase” “Carb_kinase” “Choline_kinase” “DAG_kinase_N”
[7] “Flavokinase” “Fucokinase” “GHMP_kinases_C” “GHMP_kinases_N” “Hexokinase_1” “Hexokinase_2"
[13] “NAD_kinase” “P-mevalo_kinase” “PI3_PI4_kinase” “Pkinase” “Pkinase_C” “Pkinase_Tyr”

Genes will be added to https://github.com/AlexsLemonade/OpenPBTA-analysis/blob/master/analyses/fusion_filtering/references/genelistreference.txt in correct format.

What input data should be used? Which data were used in the version being updated?

v14 version
pbta-fusion-starfusion.tsv.gz
pbta-fusion-arriba.tsv.gz

When do you expect the revised analysis will be completed?

1 day

Who will complete the updated analysis?

@kgaonkar6

[jaclyn-taroni]

Closed via #539. The update of these files in a data release is tracked in #543.