Table 2.

Gene sets that were significant in either or both MAGENTA and MAGMA gene set enrichment analyses

Passed multiple hypothesis correction with MAGENTA			MAGENTA						MAGMA
Population, GWAS, Gene Window Upstream/Downstream	Database: Gene set	Initial Gene Set Size	Effective Gene Set Size	Leading Edge Genes†	Proposed Number of Disease Associated Genes§	Fold-Enrichment	Uncorrected P value	Benjamini-Hochberg Corrected P value	Effective Gene set Size	Beta	Beta Std	Uncorrected P value	Benjamini-Hochberg Corrected P value
AA, PDR Analysis, 5kb/5kb	GO: REGULATION OF LIPID CATABOLIC PROCESS	52	51	26	13	2	0.0001*	0.014	52	0.2051	0.0110	0.034 5	0.823
AA, Extremes of DR Analysis, 110kb/40kb	KEGG: VEGF SIGNALING PATHWAY	76	70	29	11	1.61	0.0014*	0.018	75	0.0827	0.0053	0.2464	1.0
AA, PDR Analysis, 5kb/5kb	GO: REGULATION OF NITRIC OXIDE BIOSYNTHETIC PROCESS	53	46	23	11	1.92	0.0003*	0.022	50	0.3345	0.0175	0.0026	0.365
AA, PDR Analysis,5kb/5kb	REACTOME: METABOLISM OF LIPIDS AND LIPOPROTEINS	478	448	135	23	1.21	0.0070	0.035	452	0.0185	0.0029	0.3121	1.0
AA, PDR Analysis, 5kb/5kb	GO: TISSUE DEVELOPMENT	1518	1444	410	49	1.14	0.0008	0.038	1457	0.0147	0.0040	0.2557	1.0
AA, PDR Analysis, 5kb/5kb	REACTOME: POST TRANSLATIONAL PROTEIN MODIFICATION	188	172	59	16	1.37	0.0040*	0.040	173	0.0751	0.0073	0.0942	0.942
AA, Extremes of DR Analysis, 110kb/40kb	KEGG: APOPTOSIS	88	75	29	10	1.53	0.0063	0.041	81	0.1826	0.0122	0.0490	0.638
AA, Extremes of DR Analysis, 5kb/5kb	GO: REGULATION OF PLATELET DERIVED GROWTH FACTOR RECEPTOR SIGNALING PATHWAY	14	14	10	6	2.5	0.0003*	0.043	14	0.2568	0.0071	0.1044	0.67
Passed multiple hypothesis correction with MAGMA			MAGENTA						MAGMA
Population, GWAS, Gene Window Upstream/Downstream	Database: Gene set	Initial Gene Set Size	Effective Gene Set Size	Number of Genes Above Enrichment Cutoff	Proposed Number of Disease Associated Genes	Fold-Enrichment	Uncorrected P value	Benjamini-Hochberg Corrected P value	Effective Gene set Size	Beta	Beta Std	Uncorrected P value	Benjamini-Hochberg Corrected P value
EU, PDR Analysis, 5kb/5kb	MGI: MP0030005 increased retinal apoptosis	36	35	12	3	1.33	0.1420	0.448	35	0.5760	0.0252	0.00001*	0.0005
EU, PDR Analysis, 5kb/5kb	REACTOME: TIGHT JUNCTION INTERACTIONS	29	27	8	1	1.14	0.3590	0.599	28	0.5808	0.0227	0.0001*	0.001
EU, PDR Analysis, 5kb/5kb	MGI: MP0008507 thin retinal ganglion layer	15	15	6	2	1.5	0.1430	0.419	15	0.6837	0.0196	0.0006*	0.012
EU, PDR Analysis, 110kb/40kb	REACTOME: HDL MEDIATED LIPID TRANSPORT	15	13	4	1	1.33	0.4020	1	15	0.6126	0.0175	0.0023*	0.023
EU, PDR Analysis, 110kb/40kb	REACTOME: LIPID DIGESTION MOBILIZATION AND TRANSPORT	46	41	16	6	1.6	0.0306	0.306	45	0.3046	0.0150	0.0064	0.032
EU, PDR Analysis, 5kb/5kb	GO: VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR SIGNALING PATHWAY	74	72	23	5	1.28	0.1070	0.958	72	0.3295	0.0207	0.0003*	0.045
EU, PDR Analysis, 5kb/5kb	MGI: MP0008067 retinal ganglion cell degeneration	16	15	8	4	2	0.0175	0.359	15	0.5462	0.0157	0.0048	0.049

AA = African American, EU = European, PDR = Proliferative Diabetic Retinopathy, DR = Diabetic Retinopathy, GO = Gene Ontology, KEGG = Kyoto Encyclopedia of Genes and Genomes, REACTOME = Reactome Pathway Database, MGI = Mouse Genome Informatics (Mouse Phenotype Ontology gene sets).

^*These genes sets passed Bonferroni correction in the analysis (MAGENTA or MAGMA).

^†Number of genes above 75^th percentile enrichment cutoff.

^§Number of observed genes above enrichment cutoff minus number of expected genes above enrichment cutoff.

The Uncorrected P value for MAGENTA was taken from ‘NOMINAL_GSEA_PVAL_95PERC_CUTOFF’ in Supplementary Table 2.

Gene sets in bold pass Benjamini-Hochberg with one method and are nominal significant (uncorrected P value <0.05) with the other method.