Table: Gene sets enriched in phenotype Stage II (72 samples)

	GS follow link to MSigDB	GS DETAILS	SIZE	ES	NES	NOM p-val	FDR q-val	FWER p-val	RANK AT MAX	LEADING EDGE
1	GNF2_BNIP3L		9	-0.68	-1.63	0.027	1.000	0.776	677	tags=67%, list=16%, signal=79%
2	GNF2_MAP2K3		9	-0.64	-1.60	0.024	1.000	0.843	551	tags=56%, list=13%, signal=64%
3	GNF2_BNIP2		4	-0.79	-1.54	0.028	1.000	0.957	450	tags=50%, list=10%, signal=56%
4	GNF2_RAD23A		10	-0.59	-1.48	0.073	1.000	0.985	551	tags=50%, list=13%, signal=57%
5	GNF2_RAB3A		20	-0.52	-1.46	0.074	1.000	0.991	406	tags=30%, list=9%, signal=33%
6	GNF2_SPTA1		12	-0.54	-1.45	0.083	1.000	0.993	677	tags=50%, list=16%, signal=59%
7	GNF2_ANK1		11	-0.53	-1.40	0.089	1.000	1.000	551	tags=45%, list=13%, signal=52%
8	GNF2_SPTB		11	-0.53	-1.40	0.089	1.000	1.000	551	tags=45%, list=13%, signal=52%
9	MORF_THRA		16	-0.50	-1.40	0.077	1.000	1.000	1078	tags=69%, list=25%, signal=91%
10	GNF2_APEX1		3	-0.78	-1.38	0.102	1.000	1.000	27	tags=33%, list=1%, signal=34%
11	GNF2_NPM1		2	-0.93	-1.38	0.035	1.000	1.000	27	tags=50%, list=1%, signal=50%
12	CAR_IGFBP1		10	-0.60	-1.37	0.129	1.000	1.000	678	tags=40%, list=16%, signal=47%
13	GNF2_TAL1		11	-0.51	-1.37	0.101	1.000	1.000	551	tags=45%, list=13%, signal=52%
14	GNF2_PCAF		5	-0.67	-1.35	0.141	1.000	1.000	551	tags=60%, list=13%, signal=69%
15	GNF2_ST13		4	-0.71	-1.35	0.137	1.000	1.000	27	tags=25%, list=1%, signal=25%
16	GNF2_MAPT		22	-0.47	-1.34	0.157	1.000	1.000	406	tags=32%, list=9%, signal=35%
17	GNF2_TM4SF2		13	-0.51	-1.33	0.168	0.989	1.000	339	tags=23%, list=8%, signal=25%
18	GNF2_SPINK1		6	-0.59	-1.28	0.175	1.000	1.000	1444	tags=83%, list=34%, signal=125%
19	GNF2_EIF3S6		6	-0.60	-1.26	0.202	1.000	1.000	27	tags=17%, list=1%, signal=17%
20	GCM_RAN		24	-0.37	-1.25	0.172	1.000	1.000	700	tags=29%, list=16%, signal=35%
21	MORF_THPO		45	-0.33	-1.24	0.170	1.000	1.000	827	tags=33%, list=19%, signal=41%
22	GNF2_DAP3		7	-0.55	-1.22	0.239	1.000	1.000	27	tags=14%, list=1%, signal=14%
23	GNF2_SERPINI2		5	-0.63	-1.22	0.249	1.000	1.000	847	tags=60%, list=20%, signal=75%
24	GNF2_FBL		5	-0.57	-1.22	0.270	1.000	1.000	27	tags=20%, list=1%, signal=20%
25	CAR_HPX		10	-0.49	-1.21	0.236	1.000	1.000	678	tags=40%, list=16%, signal=47%
26	GCM_DDX11		6	-0.60	-1.21	0.279	1.000	1.000	300	tags=33%, list=7%, signal=36%
27	GCM_NCAM1		25	-0.35	-1.19	0.218	1.000	1.000	569	tags=24%, list=13%, signal=27%
28	GNF2_NS		2	-0.77	-1.19	0.284	1.000	1.000	592	tags=50%, list=14%, signal=58%
29	GNF2_CDC27		8	-0.47	-1.18	0.246	1.000	1.000	551	tags=38%, list=13%, signal=43%
30	GNF2_DNM1		34	-0.37	-1.18	0.272	1.000	1.000	406	tags=26%, list=9%, signal=29%
31	GCM_DLG1		16	-0.38	-1.18	0.222	1.000	1.000	1020	tags=38%, list=24%, signal=49%
32	GCM_FANCL		1	-0.89	-1.17	0.231	1.000	1.000	462	tags=100%, list=11%, signal=112%
33	GCM_MAP1B		14	-0.42	-1.15	0.301	1.000	1.000	489	tags=29%, list=11%, signal=32%
34	GNF2_TST		18	-0.40	-1.14	0.310	1.000	1.000	422	tags=22%, list=10%, signal=25%
35	GCM_CRKL		4	-0.62	-1.14	0.329	1.000	1.000	1526	tags=75%, list=35%, signal=116%
36	GNF2_CEBPA		10	-0.47	-1.14	0.325	1.000	1.000	422	tags=30%, list=10%, signal=33%
37	GNF2_RTN1		31	-0.37	-1.12	0.337	1.000	1.000	416	tags=29%, list=10%, signal=32%
38	GCM_SMO		8	-0.49	-1.11	0.335	1.000	1.000	749	tags=38%, list=17%, signal=45%
39	GNF2_GSTM1		18	-0.38	-1.08	0.380	1.000	1.000	678	tags=28%, list=16%, signal=33%
40	MORF_MAP3K14		33	-0.30	-1.08	0.346	1.000	1.000	1211	tags=39%, list=28%, signal=54%
41	GNF2_LCAT		19	-0.37	-1.08	0.388	1.000	1.000	678	tags=26%, list=16%, signal=31%
42	GCM_USP6		9	-0.42	-1.07	0.357	1.000	1.000	855	tags=33%, list=20%, signal=42%
43	GNF2_UBE2I		5	-0.54	-1.07	0.410	1.000	1.000	27	tags=20%, list=1%, signal=20%
44	CAR_TNFRSF25		10	-0.40	-1.06	0.370	1.000	1.000	1270	tags=60%, list=30%, signal=85%
45	GNF2_AF1Q		20	-0.36	-1.06	0.377	1.000	1.000	1030	tags=55%, list=24%, signal=72%
46	GNF2_HPN		20	-0.36	-1.04	0.418	1.000	1.000	678	tags=25%, list=16%, signal=30%
47	GCM_MLL		12	-0.39	-1.02	0.436	1.000	1.000	1096	tags=50%, list=25%, signal=67%
48	MORF_MYL3		24	-0.29	-1.01	0.433	1.000	1.000	1091	tags=42%, list=25%, signal=56%
49	GNF2_IGFBP1		7	-0.45	-1.00	0.450	1.000	1.000	969	tags=43%, list=23%, signal=55%
50	MORF_DAP3		12	-0.39	-1.00	0.478	1.000	1.000	517	tags=25%, list=12%, signal=28%
51	GNF2_PA2G4		3	-0.61	-1.00	0.537	1.000	1.000	1659	tags=100%, list=39%, signal=163%
52	MORF_MYST2		11	-0.36	-0.99	0.477	1.000	1.000	636	tags=27%, list=15%, signal=32%
53	MORF_FEN1		7	-0.45	-0.99	0.492	1.000	1.000	1821	tags=57%, list=42%, signal=99%
54	CAR_MLANA		16	-0.32	-0.98	0.471	1.000	1.000	1363	tags=56%, list=32%, signal=82%
55	MORF_MAP2K7		59	-0.27	-0.96	0.489	1.000	1.000	1091	tags=41%, list=25%, signal=54%
56	MORF_DMPK		47	-0.26	-0.96	0.505	1.000	1.000	816	tags=28%, list=19%, signal=34%
57	CAR_WBSCR22		11	-0.35	-0.96	0.490	1.000	1.000	1261	tags=55%, list=29%, signal=77%
58	MORF_BUB1B		4	-0.55	-0.95	0.586	1.000	1.000	928	tags=50%, list=22%, signal=64%
59	MORF_CTSB		59	-0.27	-0.95	0.517	1.000	1.000	827	tags=29%, list=19%, signal=35%
60	GCM_RAP2A		6	-0.40	-0.95	0.506	1.000	1.000	247	tags=17%, list=6%, signal=18%
61	GNF2_HPX		22	-0.32	-0.95	0.531	1.000	1.000	678	tags=23%, list=16%, signal=27%
62	MORF_ITGA2		18	-0.32	-0.94	0.523	1.000	1.000	1527	tags=61%, list=36%, signal=94%
63	GNF2_PRDX2		5	-0.42	-0.93	0.546	1.000	1.000	87	tags=20%, list=2%, signal=20%
64	MORF_SP3		5	-0.50	-0.93	0.586	1.000	1.000	1339	tags=60%, list=31%, signal=87%
65	GCM_PTPRD		10	-0.35	-0.93	0.545	1.000	1.000	700	tags=30%, list=16%, signal=36%
66	GCM_CHUK		4	-0.48	-0.93	0.570	1.000	1.000	855	tags=50%, list=20%, signal=62%
67	MORF_MSH2		2	-0.61	-0.92	0.648	1.000	1.000	1659	tags=100%, list=39%, signal=163%
68	MORF_UNG		4	-0.47	-0.92	0.579	1.000	1.000	1821	tags=75%, list=42%, signal=130%
69	GNF2_MMP1		11	-0.36	-0.91	0.583	1.000	1.000	404	tags=27%, list=9%, signal=30%
70	GCM_PPM1D		4	-0.48	-0.91	0.580	1.000	1.000	1085	tags=50%, list=25%, signal=67%
71	GNF2_CDKN1C		7	-0.40	-0.91	0.581	1.000	1.000	494	tags=29%, list=11%, signal=32%
72	MORF_CNTN1		21	-0.28	-0.91	0.602	1.000	1.000	636	tags=24%, list=15%, signal=28%
73	MORF_PDPK1		14	-0.30	-0.90	0.614	1.000	1.000	636	tags=21%, list=15%, signal=25%
74	MORF_ESPL1		4	-0.48	-0.89	0.637	1.000	1.000	1659	tags=50%, list=39%, signal=81%
75	MORF_WNT1		29	-0.25	-0.87	0.625	1.000	1.000	1016	tags=31%, list=24%, signal=40%
76	MORF_RBM8A		21	-0.26	-0.87	0.688	1.000	1.000	339	tags=14%, list=8%, signal=15%
77	GNF2_CKS1B		1	-0.64	-0.86	0.695	1.000	1.000	1545	tags=100%, list=36%, signal=156%
78	GNF2_CDH3		6	-0.40	-0.85	0.652	1.000	1.000	980	tags=50%, list=23%, signal=65%
79	GNF2_SERPINB5		6	-0.40	-0.85	0.652	1.000	1.000	980	tags=50%, list=23%, signal=65%
80	MORF_EI24		11	-0.37	-0.85	0.634	1.000	1.000	1339	tags=45%, list=31%, signal=66%
81	GNF2_EGFR		7	-0.36	-0.85	0.664	1.000	1.000	494	tags=29%, list=11%, signal=32%
82	MORF_RFC4		7	-0.42	-0.84	0.646	1.000	1.000	1323	tags=43%, list=31%, signal=62%
83	GCM_PTK2		27	-0.24	-0.84	0.710	1.000	1.000	1488	tags=41%, list=35%, signal=62%
84	GNF2_MYL2		8	-0.35	-0.83	0.696	1.000	1.000	1102	tags=38%, list=26%, signal=50%
85	MORF_BCL2L11		59	-0.21	-0.82	0.773	1.000	1.000	922	tags=31%, list=21%, signal=38%
86	GNF2_MLH1		1	-0.61	-0.82	0.769	1.000	1.000	1659	tags=100%, list=39%, signal=163%
87	MORF_RAB5A		6	-0.36	-0.82	0.702	1.000	1.000	241	tags=17%, list=6%, signal=18%
88	MORF_BUB1		3	-0.49	-0.82	0.738	1.000	1.000	1659	tags=67%, list=39%, signal=108%
89	MORF_SUPT3H		103	-0.20	-0.82	0.795	1.000	1.000	1091	tags=33%, list=25%, signal=43%
90	MORF_CD8A		41	-0.23	-0.81	0.751	1.000	1.000	1091	tags=37%, list=25%, signal=49%
91	MORF_MDM2		78	-0.20	-0.81	0.805	1.000	1.000	827	tags=26%, list=19%, signal=31%
92	GCM_DFFA		3	-0.47	-0.80	0.727	1.000	1.000	462	tags=33%, list=11%, signal=37%
93	MORF_RAD51L3		114	-0.19	-0.80	0.850	1.000	1.000	1091	tags=32%, list=25%, signal=41%
94	MORF_PTPRR		33	-0.26	-0.80	0.754	1.000	1.000	827	tags=30%, list=19%, signal=37%
95	GCM_RBM8A		5	-0.39	-0.79	0.731	1.000	1.000	316	tags=20%, list=7%, signal=22%
96	MORF_PTPRB		83	-0.19	-0.79	0.815	1.000	1.000	922	tags=27%, list=21%, signal=33%
97	MORF_MAGEA9		124	-0.18	-0.78	0.858	1.000	1.000	1113	tags=31%, list=26%, signal=41%
98	MORF_IFNA1		68	-0.20	-0.78	0.844	1.000	1.000	827	tags=26%, list=19%, signal=32%
99	MORF_IL4		63	-0.21	-0.78	0.794	1.000	1.000	1085	tags=33%, list=25%, signal=44%
100	MORF_TPR		12	-0.30	-0.78	0.733	1.000	1.000	931	tags=33%, list=22%, signal=42%
101	MORF_TERF1		5	-0.38	-0.77	0.744	1.000	1.000	1065	tags=40%, list=25%, signal=53%
102	GCM_BCL2L1		2	-0.45	-0.76	0.784	1.000	1.000	669	tags=50%, list=16%, signal=59%
103	MORF_BAG5		2	-0.49	-0.76	0.813	1.000	1.000	1151	tags=50%, list=27%, signal=68%
104	MORF_ATF2		95	-0.19	-0.76	0.876	1.000	1.000	827	tags=25%, list=19%, signal=31%
105	GNF2_TTN		4	-0.39	-0.75	0.756	1.000	1.000	650	tags=50%, list=15%, signal=59%
106	GNF2_MMP11		9	-0.31	-0.74	0.762	1.000	1.000	494	tags=22%, list=11%, signal=25%
107	GNF2_GLTSCR2		1	-0.55	-0.74	0.882	1.000	1.000	1939	tags=100%, list=45%, signal=182%
108	GCM_MYST2		11	-0.27	-0.71	0.831	1.000	1.000	317	tags=18%, list=7%, signal=20%
109	MORF_CASP2		21	-0.22	-0.70	0.874	1.000	1.000	636	tags=19%, list=15%, signal=22%
110	MORF_AATF		13	-0.26	-0.70	0.848	1.000	1.000	517	tags=23%, list=12%, signal=26%
111	MORF_ARAF1		15	-0.26	-0.69	0.871	1.000	1.000	1671	tags=53%, list=39%, signal=87%
112	GCM_UBE2N		12	-0.26	-0.69	0.883	1.000	1.000	985	tags=33%, list=23%, signal=43%
113	GNF2_XRCC5		4	-0.35	-0.69	0.841	1.000	1.000	517	tags=25%, list=12%, signal=28%
114	MORF_PRKDC		10	-0.28	-0.69	0.848	1.000	1.000	1340	tags=50%, list=31%, signal=72%
115	MORF_SNRP70		6	-0.33	-0.69	0.838	1.000	1.000	517	tags=33%, list=12%, signal=38%
116	MORF_LCAT		37	-0.19	-0.69	0.928	1.000	1.000	293	tags=11%, list=7%, signal=12%
117	GNF2_KISS1		11	-0.26	-0.68	0.870	1.000	1.000	494	tags=18%, list=11%, signal=20%
118	GNF2_TIMP2		11	-0.26	-0.68	0.870	1.000	1.000	494	tags=18%, list=11%, signal=20%
119	MORF_RAB3A		27	-0.21	-0.68	0.890	1.000	1.000	1636	tags=52%, list=38%, signal=83%
120	GNF2_MATK		5	-0.32	-0.68	0.879	1.000	1.000	1317	tags=60%, list=31%, signal=86%
121	GNF2_BUB3		2	-0.41	-0.65	0.896	1.000	1.000	517	tags=50%, list=12%, signal=57%
122	GCM_SUFU		5	-0.31	-0.65	0.898	1.000	1.000	316	tags=20%, list=7%, signal=22%
123	MORF_MBD4		7	-0.31	-0.65	0.879	1.000	1.000	1500	tags=57%, list=35%, signal=88%
124	MORF_CDH4		43	-0.18	-0.62	0.959	1.000	1.000	816	tags=26%, list=19%, signal=31%
125	MORF_PTPN11		11	-0.27	-0.61	0.877	1.000	1.000	3149	tags=100%, list=73%, signal=373%
126	MORF_ZNF10		14	-0.22	-0.60	0.943	1.000	1.000	418	tags=14%, list=10%, signal=16%
127	GCM_DPF2		4	-0.29	-0.60	0.947	1.000	1.000	1295	tags=50%, list=30%, signal=71%
128	GNF2_ZAP70		5	-0.30	-0.58	0.910	1.000	1.000	882	tags=40%, list=21%, signal=50%
129	MORF_PHB		15	-0.23	-0.58	0.949	1.000	1.000	284	tags=13%, list=7%, signal=14%
130	MORF_RAB6A		5	-0.29	-0.58	0.931	1.000	1.000	3038	tags=100%, list=71%, signal=340%
131	GCM_NUMA1		4	-0.29	-0.55	0.945	1.000	1.000	3053	tags=100%, list=71%, signal=345%
132	GCM_MYCL1		4	-0.27	-0.53	0.984	1.000	1.000	1295	tags=50%, list=30%, signal=71%
133	GCM_RAF1		6	-0.24	-0.53	0.970	1.000	1.000	3255	tags=100%, list=76%, signal=411%
134	CAR_MYST2		9	-0.21	-0.53	0.980	1.000	1.000	1363	tags=56%, list=32%, signal=81%
135	MORF_RRM1		11	-0.22	-0.50	0.961	1.000	1.000	592	tags=18%, list=14%, signal=21%
136	MORF_TTN		13	-0.17	-0.48	0.984	1.000	1.000	1501	tags=46%, list=35%, signal=71%
137	GCM_HBP1		5	-0.25	-0.47	0.979	0.998	1.000	462	tags=20%, list=11%, signal=22%
138	GCM_GSPT1		12	-0.17	-0.45	0.994	0.995	1.000	1412	tags=42%, list=33%, signal=62%