Closed allaway closed 4 years ago
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 :)
seems like sunitnib (that has come up multiple times) is in the clinical trials for both NF2 as well as NF1 (pNFs)
NF2: https://www.nf2is.org/sunitinib.php NF1: https://clinicaltrials.gov/ct2/show/NCT01402817 (this was terminated due to patient death related to drug)
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?
We can try changing the threshold - or - as we discussed in person just now
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?
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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?
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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.