l - People

!
FN (false negatives): Number of residues which were test negatives and gold standard
positives.
Population: All of the residues in the HAG. We will call the number of these residues D.
Sensitivity (true positive rate) = TP / (TP + FN) = TP / H. This is the ratio of true
positives to gold standard positives.
Specificity (true negative rate) = TN / (TN + FP) = TN / (D - H). This is the ratio of true
negatives to gold standard negatives.
Null hypothesis: The statistical hypothesis that the set of test positives is not different
from the population in a statistically significant fashion.
Alternate hypothesis: The hypothesis that the set of test positives is different from the
population in a statistically significant fashion.
p-value: This is the probability that a set of residues numbering as many residues as are
in the test positive set, and selected randomly from the population, would contain TP or
more gold standard positive residues. If the p-value is above 0.05 we conventionally
accept the null hypothesis, otherwise we reject the null hypothesis in favor of the
alternate hypothesis. Clearly, the smaller the p-value the better the predictor.
The p-value is computed for all predictors in this study using the cumulative
hypergeometric function,
p-value =
M
"
x=TP
HYP(H,D,x, M)
123