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On the Report page, the sections are difficult to interpret for novices (and difficult for me to recall from week to week). It would help to add a block of text like this for each tool.
Calculation results which are "out of range" should be color highlighted.
Some starting points for discussion:
PathProx gives.... (note ROC curve importance)
ScanNet gives (per-residue) likelihood of being P-P-I site
On the Report page, the sections are difficult to interpret for novices (and difficult for me to recall from week to week). It would help to add a block of text like this for each tool.
Calculation results which are "out of range" should be color highlighted.
Some starting points for discussion:
PathProx gives.... (note ROC curve importance)
ScanNet gives (per-residue) likelihood of being P-P-I site
Values >0.5 are considered positive. Please see https://pubmed.ncbi.nlm.nih.gov/36116806/
MuSiteDeep (per-residue) PTM gives Gene,Native Residue,PTM Residue,Type,Probability (best results for: pTyr,NGly,N-Ace,M-Arg,M-Lys,Palm-Cys,H-Lys,Sumoyl; Lower PR-AUC: P-Ser/Thr,O-gly,Ubiq,H-Pro) Please see https://pubmed.ncbi.nlm.nih.gov/32324217/
DiGePred predicts digenic interactions with lower false positive rate than DIEP, and displays the evidence in the mouse-over.
Values > .50 are positive. Please see https://pubmed.ncbi.nlm.nih.gov/34529933/
DIEP has higher sensitivity than DiGePred (89% v 42%) with higher FP rate.
Please see https://pubmed.ncbi.nlm.nih.gov/35891796/
Rate4Site (from ConSurf) gives zscores; lower score is more conserved than avg.
Please see https://pubmed.ncbi.nlm.nih.gov/12169533/
COSMIS gives zscores; lower score (red) less tolerant to missense mutations
pathogenics have median -1.1, high-conf (p-value<0.01) below -2.33
Please see https://pubmed.ncbi.nlm.nih.gov/35672414/
Add shading to any scores that are above the threshold for that tool.
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