Table 2.

Pattern-based pathway analysis on Illumina human HT-12 v4 arrays and Affymetrix HTA 2.0 arrays using Cytoscape based BiNGO

Analysis Mode	Pattern	GO ID	Description	x	n	X	N	P Value	FDR P Value
Illumina	5	5634	Nucleusa	74	5183	130	17,783	3.30×10−11	6.90×10−08
		50794	Regulation of cellular process	80	6221	130	17,783	5.50×10−10	5.76×10−07
		50789	Regulation of biologic process	81	6551	130	17,783	3.02×10−09	1.35×10−06
	6	5739	Mitochondriona	87	1273	342	17,780	2.80×10−26	7.93×10−23
		44444	Cytoplasmic part	169	5147	342	17,780	7.02×10−16	9.92×10−13
		44429	Mitochondrial parta	45	612	342	17,780	9.48×10−15	8.94×10−12
	9	5634	Nucleusa	143	5181	317	17,767	9.40×10−10	2.19×10−06
		44451	Nucleoplasm part	34	585	317	17,767	1.49×10−09	2.19×10−06
		5515	Protein binding	195	8110	317	17,767	7.50×10−09	5.48×10−06
	7 and 13	5739	Mitochondriona	34	1272	191	17,785	6.66×10−07	1.34×10−03
	5 and 9	5634	Nucleusa	215	5180	443	17,761	2.83×10−18	1.01×10−14
		50794	Regulation of cellular process	239	6210	443	17,761	1.04×10−16	1.85×10−13
		50789	Regulation of biologic process	246	6540	443	17,761	4.26×10−16	5.08×10−13
	6, 7, and 13	5739	Mitochondriona	121	1273	533	17,774	3.82×10−31	1.33×10−27
		44444	Cytoplasmic part	248	5147	533	17,774	2.30×10−18	4.01×10−15
		44429	Mitochondrial parta	62	612	533	17,774	3.06×10−17	3.55×10−14
Affymetrix	2	5739	Mitochondriona	274	1272	1357	17,736	9.68×10−61	5.19×10−57
		43231	Intracellular membrane-bounded organellea	899	8330	1357	17,736	3.57×10−50	9.58×10−47
		43227	Membrane-bounded organellea	899	8337	1357	17,736	5.61×10−50	1.00×10−46
	4	5634	Nucleusa	543	5167	1020	17,727	6.00×10−62	3.06×10−58
		10468	Regulation of gene expression	364	2920	1020	17,727	1.49×10−53	3.79×10−50
		60255	Regulation of macromolecule metabolic process	398	3369	1020	17,727	2.30×10−53	3.92×10−50
	1 and 2	5739	Mitochondriona	288	1272	1468	17,733	3.07×10−61	1.70×10−57
		43231	Intracellular membrane-bounded organelle	976	8330	1468	17,733	9.56×10−56	2.65×10−52
		43227	Membrane-bounded organelle	976	8337	1468	17,733	1.57×10−55	2.90×10−52
	3 and 4	50794	Regulation of cellular process	728	6201	1346	17,713	2.90×10−50	1.69×10−46
		5634	Nucleusa	640	5167	1346	17,713	8.47×10−50	2.47×10−46
		50789	Regulation of biologic process	750	6530	1346	17,713	1.55×10−48	3.01×10−45

Top three pathways for each pattern with FDR P<0.01; detail in Supplemental Tables 8 and 9. GO, gene ontology; x, number of gene IDs identified in the designated pathway among input gene IDs; n, number of known gene IDs in the designated pathway; X, number of input gene IDs selected by BiNGO; N, number of background gene IDs selected from the Gene Ontology pool by BiNGO.

^aHighly replicated pathway.