Revision: Run and assess GSVA results at threshold

[sjspielman]

To assess the affects of tumor purity on our results, we should re-run GSVA, considering only samples that have tumor_fraction>= median tumor fraction (https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1622).

We should then assess how well the following results hold up:

• MYC upregulation in HGG, DMG, MB, and ATRT --> upregulation of MYC + E2F targets+ G2M (cell cycle phase following S phase) in MBs, ATRTs, and HGGs. LGGs downregulated here.
  • https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/b0fdf6f24fe9c021f22e8b7da348708f68877ee5/content/03.results.md?plain=1#L274-L276
• upregulation of cytokines ifn-gamma, il-1, il-6 in Schwannomas and neurofibromas
  • https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/b0fdf6f24fe9c021f22e8b7da348708f68877ee5/content/03.results.md?plain=1#L277
• upregulation of IFN-alpha and IFN-gamma in LGGs and craniopharyngiomas compared to medulloblastoma and ependymoma which show IFN-alpha downregulation
  • https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/b0fdf6f24fe9c021f22e8b7da348708f68877ee5/content/03.results.md?plain=1#L279

[sjspielman]

@jharenza I wonder if you could weigh in on something really quickly - I'm going through all of these (almost done!!) to see if trends identified in the MS are broadly consistent after tumor purity filtering (preview: so far consistent!).

But, I realize our wording in this MS sentence might need some clean-up in general since I'm not exactly sure what it's referring to: https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/b0fdf6f24fe9c021f22e8b7da348708f68877ee5/content/03.results.md?plain=1#L279

We also observed significant upregulation of pro-inflammatory cytokines IFN$\alpha$ and IFN$\gamma$ in LGGs and craniopharyngiomas compared to medulloblastoma and ependymoma tumors (Bonferroni-corrected p < 0.05), both of which showed significant down-regulation of these cytokines (Figure {@fig:Fig5}B).

Is this making a statement specifically about comparing LGG to MB (for example, and so on..), or a broad statement overall LGG comparisons, MB comparisons, etc to any other cancer group?

[jharenza]

sure - this is saying: up in in LGG compared to MB up in LGG compared to EPN up in Cranio compared to MB up in cranio cpmpared to EPN

based on how i wrote it 😬