Identifying collateral and synthetic lethal vulnerabilities within the DNA-damage response

BMC Bioinformatics

Table 5 Validation of the SL gene pairs identified by means of the hypergeometric test on CNA profiles

Gene	#pairs	hyp-PW	hyp-GARP	our-PW	Our-GARP
PTEN	71	13	19	43	49
TP53	51	14	0	32	33
BRCA2	34	0	4	15	0
ATM	26	3	10	15	18
CDH1	33	5	4	15	16
RB1	52	7	19	35	44
MSH3	18	0	5	22	8

For each DDR gene, we ranked the predictions and considered the top pairs, in the same number as the predictions of our method. The we validated such predictions with both the pathway (hyp-PW) and the gene essentiality (hyp-GARP) methods. We report the summary of the predictions for 7 DDR genes; all the results refer to a p value < 0.05. In order to facilitate the comparison with our method the table also reports the our-PW value (which corresponds to the PW value of Table 4) and our-GARP value (which corresponds to the garpDD value of Table 3)

ISSN: 1471-2105