Table 3.

Functional modules and informative proteins found in the yeast interaction network

module ID	module size	informative proteins	function	-log(p-value)
2	81	YLR147c, YGR091w	mRNA processing – splicing	59.88
3	240	YBR160w	mitotic cell cycle	35.37
4	63	YER012w	protein degradation – proteasome	26.48
5	95	YDL140c	mRNA synthesis – general transcription activity	45.23
6	76	YCR093w, YGR134w	mRNA synthesis – transcriptional control	32.23
7	90	YJR022w, YOL149w	mRNA processing – splicing	50.30
13	89	YGR119c	nuclear transport	48.42
18	67	YDR448w	mRNA synthesis – transcriptional control	42.64
19	21	YJR121w	energy generation	28.35
24	50	YGR013w	mRNA processing – splicing	57.60
27	74	YOR181w	actin cytoskeleton	29.85
28	65	YGL172w	RNA transport	44.04
29	30	YLR127c, YDR118w	protein modification – ubiquitination	29.58
39	65	YLR347c	nuclear transport	57.92
47	75	YLR229c	budding and cell polarity	44.52
61	53	YGL092w	structural protein binding	24.01
63	40	YPR181c	vesicular transport – ER to Golgi transport	39.22
65	41	YKL145w	protein modification – proteolytic processing	29.89
71	58	YBL050w	vesicular transport – vesicle fusion	26.75
76	36	YBR088c	DNA repair	23.09
78	48	YLR335w	nuclear transport	49.21
83	46	YJL041w	RNA transport	42.93
89	28	YPR041w	protein synthesis – translation initiation	36.63
95	36	YIL109c	vesicular transport – ER to Golgi transport	41.47
109	52	YER172c	mRNA processing – splicing	53.47
101	24	YGL153w	peroxisome creation	24.57
111	23	YDR244w	peroxisomal transport	26.33
122	62	YHR165c	mRNA processing – splicing	59.90
141	24	YBL023c	DNA synthesis – ori recognition	29.35
151	31	YOR076c	nucleotide metabolism – RNA degradation	31.01
153	39	YDR227w	DNA modification – DNA conformation	24.55
161	28	YLR175w	rRNA processing	21.22
181	33	YOR121w	transmembrane signal transduction	17.46
183	23	YNL102w	DNA synthesis – polymerization	16.01
185	10	YDR016c	cell cycle – chromosomal cycle	14.49

Flow-based modularization algorithm was implemented with 200 informative proteins and 0.1 as a minimum flow threshold. The input network was weighted by semantic interactivity. 35 output modules are listed with their informative proteins, functions and -log(p-value). Some modules have two informative proteins because they were merged during the post-process.