Table 1.

Data source

Data categories	Volume of input data	Original sources/tools	Volume of original data	Download date
PPI network	156,459 PPIs	HPRD	39,240 PPIs	Mar. 3, 2013
		BioGRID	129,180 PPIs	Mar. 3, 2013
		homoMINT	33,502 PPIs	Mar. 3, 2013
		IntAct	95,746 PPIs	Mar. 3, 2013
		Human Signalling Network	59,111 PPIs	Mar. 3, 2013
Gene expression data	53 GDSes	GEO	57 GDSes	Apr. 7, 2011
Known cancer genes	37 genes	OMIM	30 genes	Mar. 3, 2013
		CGC	19 genes	Mar. 3, 2013
GO term (BP)	80 terms	DAVID*	50 terms	Mar. 3, 2013
		GOEAST*	50 terms	Mar. 3, 2013
		GOstats*	50 terms	Mar. 3, 2013
		Cancer-hallmark GO terms	9 terms	Mar. 3, 2013

* For the known breast cancer gene set, three tools were used to perform the enrichment analyses of GO terms in the BP sub-ontology: DAVID (http://david.abcc.ncifcrf.gov/home.jsp), GOEAST (http://omicslab.genetics.ac.cn/GOEAST/), and GOstats (R package in Bioconductor). DAVID and GOEAST are web tools; GOstats is an R package from Bioconductor. Cancer-hallmark GO terms were extracted from Table 1 of [37].