Table 3. Comparison of ProfCom GO PAH-SSc microarray data analysis using GO annotation dataset with and without the human protein annotations submitted by the Cardiovascular Initiative.

		GO dataset including Cardiovascular Initiative annotations			GO dataset without Cardiovascular Initiative annotations
GO ID	GO term	p-value	Study count(t = 265)	Population count(t = 18257)	p-value	Study count(t = 265)	Population count(t = 18252)
GO:0032496	response to lipopolysaccharide	5.45E-05	12	107	1.22E-03	10	95
GO:0006954	inflammatory response	2.03E-04	16	224	1.59E-02	13	214
GO:0045768	positive regulation of anti-apoptosis	5.28E-04	7	34	2.06E-03	6	27
GO:0045429	postive regulation of nitric oxide biosynthetic process	1.75E-03	6	26	#N/A	#N/A	#N/A
GO:0006955	immune response	1.82E-03	23	510	1.30E-03	23	502
GO:0048661	positive regulation of smooth muscle cell proliferation	2.22E-03	6	27	6.23E-03	5	19
GO:0014070	response to organic cyclic substance	3.02E-03	10	104	2.82E-03	10	104
GO:0050900	leukocyte migration	3.60E-03	10	106	1.94E-02	9	103
GO:0051412	response to corticosterone stimulus	6.69E-03	5	19	6.23E-03	5	19
GO:0019221	cytokine-mediated signaling pathway	9.66E-03	13	203	1.32E-01	11	194

Significant p-values are highlighted in bold text. GO processes with p-values<0.01 identified by ProfCom GO [25] are considered as significantly enriched. t  =  number of protein IDs.