Table 3. Biological pathways and diseases.

A
Ingenuity pathways				KEGG pathways			GeneGO pathways
#	Top canonical pathways	P-value	Ratio	Pathway name	Enrichment score	Enrichment P-value	Process networks	Ratio	P-value
Prioritization CFG score ⩾4 (n=412 genes)
1	G-protein coupled receptor signaling	6.27e−14	10.6% 28/264	GABAergic synapse	10.8524	1.94e−05	Cell adhesion_Amyloid proteins	27/195	4.78E-09
2	cAMP-mediated signaling	2.04e−11	10.3% 23/223	Amoebiasis	10.7231	2.20e−05	Reproduction_Gonadotropin regulation	27/199	7.49E-09
3	Glucocorticoid receptor signaling	6.84e−11	8.9% 25/281	Melanogenesis	10.2992	3.37e−05	Reproduction_GnRH signaling pathway	22/166	3.00E-07
4	CREB signaling in neurons	1.01e−10	11.2% 20/179	Pathogenic Escherichia coli infection	9.03249	0.000119	Development_Hedgehog signaling	28/254	3.65E-07
5	Cardiac hypertrophy signaling	2.88e−10	9.5% 22/232	Chemokine signaling pathway	8.82088	0.000148	Cytoskeleton_Regulation of cytoskeleton rearrangement	23/183	4.22E-07
Validation stepwise (n=204 genes)
1	B-cell receptor signaling	1.01e−08	7.2% 13/181	Focal adhesion	10.5307	2.67e−05	Signal transduction_WNT signaling	19/177	8.10E-10
2	Ovarian cancer signaling	3.31e−08	8.3% 11/133	Colorectal cancer	10.3054	3.35e−05	Cell cycle_G1-S Growth factor regulation	18/195	2.62E-08
3	Glucocorticoid receptor signaling	3.97e−08	5.3% 15/281	GABAergic synapse	8.60276	0.000184	Reproduction_Gonadotropin regulation	18/199	3.60E-08
4	Colorectal cancer metastasis signaling	4.00e−08	5.8% 14/241	mTOR signaling pathway	8.47678	0.000208	Reproduction_GnRH signaling pathway	16/166	9.05E-08
5	G12/13 signaling	1.12e−07	8.5% 10/118	Chagas disease (American trypanosomiasis)	7.66796	0.000468	Neurophysiological process_Transmission of nerve impulse	18/212	9.58E-08
Validation nominally significant (n=143 genes)
1	B-cell receptor signaling	1.95e−07	5.5% 10/181	Focal adhesion	8.91242	0.000135	Cell cycle_G1-S Growth factor regulation	16/195	3.62E-09
2	Cholecystokinin/gastrin-mediated signaling	3.18e−07	7.5% 8/106	mTOR signaling pathway	8.34274	0.000238	Inflammation_Histamine signaling	14/213	6.04E-07
3	G12/13 signaling	7.25e−07	6.8% 8/118	Wnt signaling pathway	7.1443	0.000789	Signal transduction_WNT signaling	12/177	2.99E-06
4	Glucocorticoid receptor signaling	1.46e−06	3.9% 11/281	Amphetamine addiction	6.67296	0.001265	Cell cycle_G1-S Interleukin regulation	10/128	6.05E-06
5	Ovarian cancer signaling	1.80e−06	6.0% 8/133	Neurotrophin signaling pathway	6.54296	0.00144	Cell adhesion_Amyloid proteins	12/195	8.17E-06
Validation Bonferroni significant (n=76 genes)
1	B-cell receptor signaling	2.38e−06	3.9% 7/181	mTOR signaling pathway	11.496	1.02E-05	Cell cycle_G1-S Growth factor regulation	9/195	2.34E-05
2	G12/13 signaling	2.70e−06	5.1% 6/118	Arginine and proline metabolism	8.02409	0.000327	Reproduction_Gonadotropin regulation	8/199	1.82E-04
3	IL-17A signaling in airway cells	2.71e−06	7.6% 5/66	Focal adhesion	7.79535	0.000412	Inflammation_IL-4 signaling	6/115	3.12E-04
4	IL-8 signaling	3.06e−06	3.7% 7/188	Pathways in cancer	7.05537	0.000863	Cell cycle_G1-S Interleukin regulation	6/128	5.55E-04
5	Integrin signaling	4.76e−06	3.5% 7/201	Renal cell carcinoma	6.07809	0.002293	Inflammation_IL-12,15,18 signaling	4/59	1.28E-03

B
Ingenuity				GeneGO
#	Diseases and disorders	P-value	# Molecules	Diseases	P-value	Ratio
Prioritization CFG score ⩾4 (n=412 genes)
1	Neurological disease	4.31e−06—5.54e−24	174	Psychiatry and psychology	4.65e−50	156/1919
2	Psychological disorders	2.69e−06—7.71e−24	123	Mental disorders	5.89e−50	143/1614
3	Organismal injury and abnormalities	4.52e−06—1.23e−21	361	Mood disorders	3.69e−37	88/797
4	Skeletal and muscular Disorders	4.52e−06—9.92e−21	129	Schizophrenia	4.28e−34	90/914
5	Cancer	4.37e−06—2.00e−20	359	Schizophrenia and disorders with psychotic features	6.01e−34	90/918
Validation stepwise (n=204 genes)
1	Organismal injury and abnormalities	s 2.11e−04—1.23e−13	178	Psychiatry and psychology	1.77e−23	76/1919
2	Cancer	2.20e−04—5.41e−13	176	Mental disorders	1.23e−21	67/1614
3	Neurological disease	1.31e−04—1.07e−12	81	Mood disorders	4.02e−21	47/797
4	Psychological disorders	1.31e−04—1.07e−12	63	Depressive disorder, major	1.06e−18	37/546
5	Tumor morphology	1.87e−04—1.83e−12	38	Depressive disorder	2.44e−18	37/560
Validation nominally significant (n=143 genes)
1	Cancer	4.75e−04—2.43e−12	122	Wounds and injuries	2.49e−17	39/993
2	Organismal injury and abnormalities	4.75e−04—2.43e−12	123	Colonic diseases	2.52e−13	77/4479
3	Tumor morphology	2.27e−04—2.43e−12	31	Psychiatry and psychology	5.32e−13	47/1919
4	Cardiovascular disease	4.28e−04—1.25e−09	36	Connective tissue diseases	8.73e−13	50/2177
5	Developmental disorder	2.27e−04—1.25e−09	28	Pathologic processes	1.75e−12	56/2709
Validation Bonferroni significant (n=76 genes)
1	Cancer	1.27e−03—1.06e−10	68	Wounds and injuries	3.16e−15	27/993
2	Organismal injury and abnormalities	1.27e−03—1.06e−10	68	Pathologic processes	6.22e−13	39/2709
3	Tumor morphology	8.81e−04—1.65e−10	22	Psychiatry and psychology	6.32e−13	33/1919
4	Cardiovascular disease	8.32e−04—4.02e−10	24	Mood disorders	1.35e−12	22/797
5	Developmental disorder	1.11e−03—4.02e−10	21	Mental disorders	1.41e−12	30/1614

Abbreviations: CFG, convergent functional genomics; KEGG, Kyoto Encyclopedia of Genes and Genomes.