moving files

[allaway]

I reran the drug target enrichment analysis but only considered approved (ie. true) drugs (list obtained from DrugCentral). This didn't work out super well, only a few drugs enriched, and they are mostly the same drugs for each LV.

[allaway]

love the bar plots, will look better when we filter drug names....

This one is for the filtered analysis, as well as the markdown we were just looking at, sorry, I didnt fill in the PR description quick enough :)

[allaway]

@sgosline http://htmlpreview.github.io/?https://raw.githubusercontent.com/Sage-Bionetworks/NF_LandscapePaper_2019/d0f089b43fa88fcd60fc5b13e84f05318e4e1fd0/results/31-viper-drug-enrichment-bydrug_Approved_only.html

[jaybee84]

seems like sunitnib (that has come up multiple times) is in the clinical trials for both NF2 as well as NF1 (pNFs)

[jaybee84]

NF2: https://www.nf2is.org/sunitinib.php NF1: https://clinicaltrials.gov/ct2/show/NCT01402817 (this was terminated due to patient death related to drug)

[sgosline]

Ahh, my git fetch didn't work at first. I think the only issue is that the dot plots look strange with so few dots. Would it be useful to use the qvalue instead of the p.adjust?

[allaway]

We can try changing the threshold - or - as we discussed in person just now

• try a bigger list of drugs (but not as big as the first list, where we were looking at all of the target space). I think filtering for FDA-approved drugs cost us a lot of target diversity, so we get a lot of the same drugs with the same few targets...

On Wed, Dec 18, 2019 at 9:27 AM Sara JC Gosline notifications@github.com wrote:

Ahh, my git fetch didn't work at first. I think the only issue is that the dot plots look strange with so few dots. Would it be useful to use the qvalue instead of the p.adjust?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Sage-Bionetworks/NF_LandscapePaper_2019/pull/93?email_source=notifications&email_token=AE3WNSFUCWBRDXNXOQCVQE3QZJMPTA5CNFSM4J4CIWLKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEHG33CY#issuecomment-567131531, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE3WNSFG744D7NHXE3A57V3QZJMPTANCNFSM4J4CIWLA .

[allaway]

where we were looking at all of the target space

Er, i mean, all of the chemical space for which we have targets.

On Wed, Dec 18, 2019 at 9:38 AM Robert Allaway robert.j.allaway@gmail.com wrote:

We can try changing the threshold - or - as we discussed in person just now - try a bigger list of drugs (but not as big as the first list, where we were looking at all of the target space). I think filtering for FDA-approved drugs cost us a lot of target diversity, so we get a lot of the same drugs with the same few targets...

On Wed, Dec 18, 2019 at 9:27 AM Sara JC Gosline notifications@github.com wrote:

Ahh, my git fetch didn't work at first. I think the only issue is that the dot plots look strange with so few dots. Would it be useful to use the qvalue instead of the p.adjust?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/Sage-Bionetworks/NF_LandscapePaper_2019/pull/93?email_source=notifications&email_token=AE3WNSFUCWBRDXNXOQCVQE3QZJMPTA5CNFSM4J4CIWLKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEHG33CY#issuecomment-567131531, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE3WNSFG744D7NHXE3A57V3QZJMPTANCNFSM4J4CIWLA .