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

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

			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

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: 25^th percentile; Q2: 50^th percentile or median; and Q3: 75^th percentile) plus the mean were used as thresholds.