Table 3.

Significant pathways: NetPEA’ vs. ORA.

Input Gene Set	# Unique Pathways		# Common Pathways
	NetPEA’	ORA	$\mathit{P}{\mathit{NetPEA}}^{\prime }\gg \mathit{P}\mathit{ORA}$	$\mathit{P}{\mathit{NetPEA}}^{\prime }\ll \mathit{P}\mathit{ORA}$	$\mathit{P}{\mathit{NetPEA}}^{\prime }\approx \mathit{P}\mathit{ORA}$
Parkinson	7	28	3	1	5
Lymphoma	16	5	4	0	6
Breast cancer [13]	11	9	0	0	9
Breast cancer [14]	5	9	1	0	11
Lung cancer [15]	28	12	1	0	2
Lung cancer [16]	27	12	1	0	11
Diabetes (down)	19	4	0	0	2
Diabetes (up)	13	2	0	0	0
Leukemia (down)	16	2	0	0	1
Leukemia (up)	15	6	0	0	4
Gender (down)	5	1	0	0	0
Gender (up)	20	3	0	0	0
p53 (down)	13	5	0	0	1
p53 (up)	27	15	0	0	9