A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila

Table 1 The network attributes and corresponding P-values for the 24 sub-networks constructed from RNAi hits.

RNAi screen [Ref]	#hits	#edges	P-value1	P-value2
Store-operated Ca2+ entry [25]	1,122	4,281	2e-05	3e-98
ERK signaling [26]	982	7,050	2e-71	<1e-229
Nuclear import of Smads [27]	683	1,321	0.07	3e-06
Protein secretion and Golgi organization [28]	645	6,597	<1e-229	<1e-229
Hh signaling pathway [29]	306	3,214	<1e-229	<1e-229
Bacterial infection [30]	286	2,803	<1e-229	<1e-229
Growth and viability [31]	281	1,871	<1e-229	<1e-229
Wnt signaling pathway [32]	167	368	5e-51	1e-92
Light-dependent CRY degradation [33]	131	197	1e-28	9e-105
Neural outgrowth genes [34]	128	414	7e-146	3e-145
Chlamydia infection [35]	126	107	2e-07	2e-17
Regulators of NFAT [36]	121	29	0.7	0.002
Multipolar divisions [37]	115	62	0.005	9e-12
Viral replication [38]	104	2,069	<1e-229	<1e-229
JAK/STAT signaling [39]	104	85	4e-09	1e-21
Mycobacterial infection [40]	76	176	1e-129	8e-117
Transcript-specific mRNA export [41]	65	146	6e-141	2e-100
Ca(2+) influx [42]	65	137	3e-123	9e-54
Muscle assembly and maintenance [43]	39	21	5e-11	5e-08
Caspase activation [44]	37	4	0.4	0.2
Mitochondrial and Peroxisomal Fission [45]	22	2	0.3	0.1
Histone pre-mRNA processing [46]	17	4	2e-04	2e-05
E2F repression [47]	15	7	2e-13	1e-39
Orai proteins [48]	15	9	1e-21	1e-30

Results are sorted based on the number of hits in descending order. The P-value1 and P-value2 are calculated by two different randomization strategies, i.e., 1) randomizing nodes and 2) randomizing edges (with fixed node degree) (see Methods for details).

ISSN: 1471-2164