Table 1.

Level two filters improve classifier accuracy

EGRIN	Agreement	Correlation	Agreement.fix	Correlation.fix	Numbers of predictions	P-value
Compendium	0.51	0.16	0.66	0.33	3145	1.00E + 00
Filter 1	0.51	0.18	0.71	0.44	2012	1.82E − 06
Filter 2	0.49	0.20	0.71	0.40	2086	3.09E − 06
Filter 3	0.49	0.16	0.69	0.36	1881	7.22E − 03
Aggregate	0.50	0.17	0.76	0.50	1015	4.96E − 11

‘Agreement’ and ‘Correlation’ refer to the fraction of time that Inferelator identifiers a regulator as an activator or repressor of a target gene and the target gene significantly decreases or increases in expression (respectively) when the regulator is deleted. The ‘.fix’ columns refer to the same measurements, but with the activator/repressor role of predictions swapped when they are significantly anti-correlated with the role revealed by the gene deletion assays. This swapping is intended to more accurately reflect the classifiers ability to identify peroxisome-related regulators. ‘P-value’ refers to the binomial P-value comparing the ‘Agreement.fix’ scores with those in the first column.