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Table 3 Precision analysis of the guilt-by-association algorithm

From: Mining tissue specificity, gene connectivity and disease association to reveal a set of genes that modify the action of disease causing genes

    Threshold for number of connections (TC)
Threshold for % disease genes among interactors (TD)    Q1
TC = 1
Q2
TC = 4
Q3
TC = 13
Mean
TC = 12
Q1 TD = 12.8 N Captured 1,943 1,391 638 683
   % Known 73.3 75.0 76.5 76.4
Q2 TD = 28.6 N Captured 1,024 563 195 219
   % Known 74.8 78.9 85.1 84.9
Q3 TD = 50.0 N Captured 251 118 16 19
   % Known 70.5 67.8 75.0 78.9
Mean TD = 35.0 N Captured 748 409 109 127
   % Known 73.4 76.3 84.4 84.2
  1. The optimality of various location parameters to be used as thresholds in the guilt-by-association algorithm was explored by computing the proportion of known (% Known) disease associated genes from the total number of captured genes (N Captured). The analysis was performed using only the 1,445 genes (out of the initial 6,151) with known disease phenotype as the set of truly disease causing, and with the remaining 4,706 declared as disease associated. The three inter-quartiles (Q1: 25th percentile; Q2: 50th percentile or median; and Q3: 75th percentile) plus the mean were used as thresholds.