Table 4.

Gene sets highly ranked across platforms. For each platform, gene sets were ranked by their association with the phenotype under study, using the p-value from the global test. Displayed are those gene sets that rank highly in the majority of platforms; for GO sets, the sum of the highest three (out of five) ranks had to be below 100; for KEGG sets, the sum of the highest four (out of five) ranks had to be below 100. Columns 1 and 2 display GO/KEGG IDs and names of the gene sets (in parentheses: GO classification: BP = biological process; MF = molecular function). Columns 3 to 7 display the ranks of the gene sets for each of the platforms.

GENE SET ID	Name	ABI	AFF	AGL	ILL	LGTC
GO
GO:0007214	gamma-aminobutyric acid signaling pathway (BP)	232	46	23	26	33
GO:0004890	GABA-A receptor activity (MF)	248	42	11	13	48
GO:0016917	GABA receptor activity (MF)	283	40	14	12	52
GO:0030594	neurotransmitter receptor activity (MF)	433	23	2	2	166
GO:0042165	neurotransmitter binding (MF)	474	22	1	1	174
GO:0006821	chloride transport (BP)	853	17	3	22	21
GO:0015698	inorganic anion transport (BP)	1022	7	21	33	76
GO:0005230	extracellular ligand-gated ion channel activity (MF)	1672	29	10	17	91
GO:0006820	anion transport (BP)	1801	8	33	34	98
GO:0015276	ligand-gated ion channel activity (MF)	1900	20	4	11	175
GO:0050900	leukocyte migration (BP)	13	898	12	69	1726
KEGG
4080	Neuroactive ligand-receptor interaction	25	1	3	2	10
4512	ECM-receptor interaction	18	9	21	16	33
2010	ABC transporters – General	27	3	15	4	53
4660	T cell receptor signaling pathway	23	16	57	8	31
760	Nicotinate and nicotinamide metabolism	58	8	4	161	20
3030	DNA polymerase	9	11	12	24	138
4514	Cell adhesion molecules (CAMs)	39	13	23	17	115
900	Terpenoid biosynthesis	13	12	54	19	62
4640	Hematopoietic cell lineage	64	4	22	9	76