l - People

test true
c
positive positive sensitivity specificity p-value
StoneHinge 1204 42 0.28 0.91 2.7E-11
HingeSeq 771 13 0.09 0.94 0.11
TLSMD 455 30 0.20 0.97 4.8E-15
hNMa 1279 37 0.24 0.91 8.7E-08
hNMb 126 31 0.20 0.99 3.2E-33
hNMc 517 26 0.17 0.96 1.7E-10
hNMd 1545 49 0.32 0.89 1.1E-11
hNMe 235 35 0.23 0.99 2.0e-29
FO1 563 8 0.05 0.96 0.32
FO1M 292 14 0.09 0.98 6.6E-06
FO 272 62 0.41 0.98 9.2E-66
Table 4.3: Performance of the predictors against the Hinge Atlas Gold annotation.
Test positives are predicted hinge locations. hNM1 and FO1 give continuous (rather than
discrete) output, normalized to range from 0 to 1 for each protein. Therefore for hNM1
and FO1 we took values below .02 and 0.1, respectively, as test positives. For HingeSeq
we took values above 0.4 as test positives. here were a total of 13259 residues in the
HAG, of which 152(13107) were Gold Standard Positives(Negatives). Therefore for the
example of StoneHinge, sensitivity was calculated as 42/152=0.28 and specificity was
(13259-1204)/13107=0.91. For the same example, p-value was computed as the
probability of finding 42 or more true positive residues in a set of 1204 residues selected
randomly and without replacement from a set of 13259, using the cumulative
hypergeometric distribution.
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