Studying alternative splicing regulatory networks through partial correlation analysis

Table 3 Gene pairs sharing gene sets and having GG, EG, or EE links

		Gene pairs having GG links (13,552)		Gene pairs having EG links (223,116)		Gene pairs having EE links (815,024)
Gene set category	No. of gene pairs sharing a gene set among a total of 53,721,795 gene pairs	No. of gene pairs also sharing gene set	p-value	No. of gene pairs also sharing gene set	p-value	No. of gene pairs also sharing gene set	p-value
c1	321,284	150	2.1 × 10^-12	1,584	1.1 × 10^-11	4,855	0.61
c2_BioCarta	30,023	40	2.0 × 10^-17	238	5.4 × 10^-20	601	2.3 × 10^-11
c2_GenMAPP	49,570	101	2.4 × 10^-56	421	4.4 × 10^-40	1,085	6.1 × 10^-31
c2_KEGG	182,069	348	1.1 × 10^-179	1,137	1.1 × 10^-38	3,048	3.1 × 10^-08
c3_miRNA	2,373,102	556	0.96	12,477	8.7 × 10^-150	49,006	< 4.9 × 10^-324
c3_promoter_known	14,479,685	4,207	1.7 × 10^-26	67,435	7.5 × 10^-261	248,414	< 4.9 × 10^-324
c3_promoter_unknown	3,186,951	915	3.5 × 10^-05	14,507	1.1 × 10^-29	55,308	1.1 × 10^-227
c4_bp	7,107,791	2,947	5.5 × 10^-163	35,289	6.9 × 10^-272	129,574	< 4.9 × 10^-324
c4_cc	6,549,156	4,418	< 4.9 × 10^-324	35,702	< 4.9 × 10^-324	127,572	< 4.9 × 10^-324
c4_mf	815,318	581	3.7 × 10^-104	4,294	4.3 × 10^-52	15,897	1.0 × 10^-209

Among the 10,366 human genes that were considered, there are 53,721,795 possible gene pairs. About 13,552 gene pairs were declared to have GG links; 223,116 gene pairs were declared to have at least one EG link; and 815,024 gene pairs were declared to have at least one EE link. The number of gene pairs that have GG, EG, or EE links and are in the same gene set is listed. The p-value of observing such a high or higher number of gene pairs that have GG, EG, or EE links and are in the same gene set was based on a hypergeometric test. Different gene set categories were considered. 'c1', genes sharing chromosomal cytogenetic bands; 'c2_BioCarta', 'c2_GenMAPP', and 'c2_KEGG', genes in the same pathways and the pathways were collected from the BioCarta, GenMAPP, or KEGG databases; 'c3_miRNA', genes sharing a microRNA binding site; 'c3_promoter_known' and 'c3_promoter_unknown', genes sharing a motif in the promoter regions and the motif matches a known transcription factor binding site or the motif does not match any known transcription factor binding site; 'c4_bp', genes sharing biological process ontology terms; 'c4_cc', genes sharing cellular component ontology terms; 'c4_mf', genes sharing molecular function ontology terms.

ISSN: 1474-760X