Proposed Analysis: Create broad histology-specific gene lists for oncoprint

[jharenza]

What are the scientific goals of the analysis?

Since the oncoprint-landscape module currently utilizes a set of genes from the interaction-plots module, and we would like to break apart the oncoprint (per #968), the lists will not include canonical fusions/CNVs observed in the histologies, nor include canonical rare mutations, so we would like to manually curate broad histology-specific gene lists for the oncoprint.

What methods do you plan to use to accomplish the scientific goals?

literature, pedcbio, previously annotated gene lists from the PPTC manuscript.

What input data are required for this analysis?

NA

How long do you expect is needed to complete the analysis? Will it be a multi-step analysis?

2-3 weeks

Who will complete the analysis (please add a GitHub handle here if relevant)?

@jharenza

What relevant scientific literature relates to this analysis?

will compile as I complete this

[jharenza]

@cbethell I created this file below, which I sent to CBTN PIs for review today, so if there are any additions, we can swap the file out afterward. I wanted to be sure we captured the sources to cite and there are currently duplicate genes due to multiple sources, so please just unique those. Hope this works!

oncoprint-goi-lists-OpenPBTA.csv

[jharenza]

close with #1046