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Another cluster (C6) contains 166 proteins with significantly higher molecular weight than the background distribution for all clusters, however no other discriminative features are evident.
SIX8 is part of a cluster with a strong secretion signal and a significantly higher percentage of aliphatic amino acids than the background distribution for all clusters.
The unsupervised clustering returns three clusters with a significantly higher secretion signal than the background distribution for all clusters (data not shown).
It is critical to stress that the choice of negative sites defines the background distribution for all features and thus determines which features will be considered useful in identifying sites.
In general, the unsupervised clustering of pathogen-associated proteins returns three clusters with a significantly higher secretion signal than the background distribution for all clusters (Mann–Whitney U test, p-value < 2.2e-16 2.2e-16
For each feature in the 35-dimensional feature vector, Mann–Whitney U tests were used to test whether the distribution within a cluster is identical to the full background distribution for all clusters and highly significant p-values for both directions (lesser ↓ and greater ↑, p-value < 2.2e-16 2.2e-16own.
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We compare the abundance of proteins in the different PINs to a background distribution of all proteins for which abundance was measured (Additional file 1: Table S3, data obtained from [ 25]).
For each expression set, co-expressed genes were defined as pairs whose Pearson correlation exceeded the 99%-quantile of the background distribution of all correlation coefficients.
We constructed a background distribution for these scores by simulating pairs of random gene lists.
For 300 of these genes the values are sampled from the same "background" normal distribution for all subtypes.
As a practical matter, background distributions for are pre-calculated for all cluster sizes less than or equal to the maximum size represented in the initial seed clusters, and additional background distributions are calculated as needed during program execution.
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