Genes - Retrospect.xlsx - Google Sheets

	A	B	C	D	E	F	G	H	I	J	K	L
1		Normalized gene RE-linked enrichment score (NGRE) is a relative enrichment of RE-linked regulatory elements in the 10-kb frame centered around gene canonical transcriptional start site. NGRE values were calculated as a ratio of RE-linked to all regulatory elements using H3K4me1, H3K4me3, H3K9ac, H3K27ac, H3K27me3, H3K9me3 chromatin tags, and transcriptional factor binding sites (TFBS) for 563 transcriptional factor proteins, established using ChIP-Seq data for 5-13 cell lines (see Sheet 2). For every functional tag, we averaged the data for all cell lines available considering weights correspond to data quality. Thus, we obtained weighted average scores separately for each his-tone tag and for TFBS (NGRE_H3K27me3, NGRE_H3K9me3, NGRE_H3K9ac, NGRE_H3K27ac, NGRE_ H3K4me3, NGRE_H3K4me1, NGRE_TFBS). Metrics of the higher level were calculteds as follows: -for active chromatin NGRE_ac = (NGRE_H3K9ac + NGRE_H3K27ac + NGRE_H3K4me3 + NGRE_H3K4me1)/4; -for heterochromatin NGRE_hc = (NGRE_H3K27me3 + NGRE_H3K9me3)/2; -NGRE_AGG = (NGRE_hc + NGRE_ac + NGRE_TFBS)/3. The ratio of the number of nonsynonymous substitutions per non-synonymous site (dN) to the number of synonymous substitutions per synonymous site (dS) was used as structural evolutionary rate metrics for individual genes. Values of dN/dS ratio for individual human genes were extracted from the previous report (A. Scally et al., 2012).
2	Gene symbol	NGRE_H3K4me1	NGRE_H3K4me3	NGRE_H3K9ac	NGRE_H3K27ac	NGRE_H3K27me3	NGRE_H3K9me3	NGRE_ac	NGRE_hc	NGRE_TFBS	NGRE_AGG	dN/dS

3	A1CF	0.61	4.61	4.58	4.46	4.85	5.91	3.56	5.38	0.77	3.24	0.12
4	A2M	0.60	4.89	4.25	3.60	4.39	3.35	3.33	3.87	0.69	2.63	0.44
5	A2ML1	1.67	11.82	12.39	10.59	14.55	13.82	9.12	14.18	1.74	8.35	0.38
6	A4GNT	1.27	8.89	13.06	7.94	12.63	13.30	7.79	12.96	1.89	7.55	0.34
7	AACS	1.53	2.59	2.68	4.61	17.62	17.25	2.85	17.44	1.39	7.22	0.12
8	AADACL2	1.33	10.55	10.21	9.64	10.06	13.56	7.93	11.81	1.73	7.16	0.27
9	AADACL3	1.28	7.47	10.09	7.54	12.11	11.05	6.60	11.58	1.49	6.56	0.52
10	AADACL4	2.22	16.95	14.48	15.59	16.48	14.97	12.31	15.72	2.89	10.31	0.41
11	AADAT	1.33	8.55	10.84	6.26	10.04	10.87	6.75	10.46	1.72	6.31	0.27
12	AAGAB	0.89	7.83	8.94	7.25	9.19	9.16	6.23	9.18	1.47	5.63	0.16
13	AAK1	1.13	8.55	10.14	6.84	8.22	11.13	6.66	9.68	1.41	5.92	0.08
14	AAMP	0.64	2.91	2.73	2.60	3.10	4.70	2.22	3.90	0.31	2.14	0.01
15	AANAT	1.16	8.43	11.14	9.89	10.85	11.47	7.66	11.16	1.07	6.63	0.21
16	AAR2	1.56	5.57	5.30	5.36	9.07	11.75	4.45	10.41	1.03	5.30	0.19
17	AARD	1.43	8.74	10.42	8.32	15.93	14.90	7.23	15.41	1.96	8.20	1.17
18	AARS	1.31	4.30	2.62	3.51	7.11	8.21	2.94	7.66	0.61	3.74	0.07
19	AASDH	1.15	7.51	7.61	6.52	8.61	8.12	5.70	8.37	1.54	5.20	0.35
20	AASDHPPT	1.11	1.73	1.28	1.36	10.57	12.59	1.37	11.58	0.74	4.57	0.07
21	ABCA1	0.78	6.87	9.17	8.59	8.56	9.19	6.35	8.88	1.12	5.45	0.11
22	ABCA12	1.04	8.42	9.71	8.74	8.53	11.40	6.98	9.97	1.80	6.25	0.19
23	ABCA13	1.09	7.63	7.83	7.62	7.83	7.86	6.04	7.84	1.37	5.08	0.64
24	ABCA2	0.33	2.88	2.38	3.04	4.36	6.51	2.16	5.43	0.55	2.71	0.03
25	ABCA4	0.44	4.78	5.06	4.93	6.81	7.75	3.80	7.28	1.13	4.07	0.15
26	ABCA5	0.55	4.53	6.12	4.30	6.03	6.06	3.88	6.05	0.77	3.56	0.21
27	ABCA7	0.73	3.33	4.03	5.02	6.17	8.00	3.28	7.08	0.76	3.71	0.16
28	ABCA8	0.93	6.81	7.85	7.50	8.49	9.50	5.77	9.00	1.35	5.37	0.36
29	ABCB1	0.64	5.01	6.01	5.25	7.37	6.56	4.23	6.97	0.97	4.05	0.27
30	ABCB11	1.38	10.52	11.68	8.65	12.20	12.56	8.06	12.38	1.52	7.32	0.18
31	ABCB5	1.82	14.77	16.36	12.72	17.74	19.37	11.42	18.55	2.78	10.91	0.28
32	ABCB7	1.04	9.27	10.90	7.33	7.66	10.87	7.14	9.26	1.48	5.96	0.16
33	ABCB8	0.92	2.83	4.42	4.85	9.09	10.37	3.25	9.73	0.68	4.55	0.21
34	ABCB9	1.95	14.06	15.54	13.28	15.84	17.43	11.21	16.63	3.08	10.31	0.03
35	ABCC11	1.19	8.72	9.16	9.10	15.45	13.72	7.04	14.58	1.46	7.69	0.48
36	ABCC2	1.69	7.57	8.77	8.76	11.28	13.07	6.70	12.17	1.75	6.87	0.38
37	ABCC3	1.15	6.19	7.79	8.47	11.37	9.29	5.90	10.33	1.15	5.79	0.20
38	ABCC4	0.72	7.39	8.13	6.00	12.16	11.55	5.56	11.86	1.42	6.28	0.14
39	ABCC5	1.60	11.06	12.52	9.96	12.13	11.72	8.79	11.93	2.07	7.59	0.03
40	ABCC8	0.53	2.62	5.03	4.86	6.44	6.52	3.26	6.48	1.14	3.63	0.04
41	ABCC9	0.55	4.79	5.23	3.17	5.45	5.99	3.44	5.72	0.92	3.36	0.04
42	ABCD2	0.79	7.92	7.24	6.39	6.43	7.54	5.59	6.99	1.38	4.65	0.12
43	ABCD3	1.06	1.21	1.23	2.57	8.91	10.29	1.52	9.60	0.74	3.95	0.11
44	ABCD4	1.25	8.02	9.89	8.08	7.96	11.36	6.81	9.66	1.85	6.11	0.18
45	ABCE1	1.64	3.19	2.08	2.30	8.96	10.04	2.30	9.50	0.71	4.17	0.00
46	ABCF3	0.87	1.93	1.60	2.13	6.38	7.60	1.63	6.99	0.59	3.07	0.05
47	ABCG1	0.54	2.35	4.70	4.03	8.95	11.56	2.91	10.25	1.30	4.82	0.14
48	ABCG2	0.62	5.50	6.33	4.49	6.44	5.63	4.23	6.03	1.02	3.76	0.25
49	ABCG4	0.80	2.05	7.34	8.57	9.72	9.65	4.69	9.68	1.27	5.21	0.02
50	ABCG5	1.24	9.89	10.32	9.30	10.99	10.86	7.69	10.92	1.90	6.84	0.37
51	ABCG8	1.06	8.46	7.69	7.87	10.62	11.70	6.27	11.16	1.69	6.37	0.18
52	ABHD10	1.01	1.44	1.56	2.28	6.09	7.50	1.57	6.80	0.68	3.01	0.31
53	ABHD12	0.30	2.51	2.97	2.48	2.63	3.65	2.06	3.14	0.47	1.89	0.12
54	ABHD12B	1.04	7.37	7.61	5.70	9.41	9.94	5.43	9.68	1.38	5.50	0.35
55	ABHD13	1.04	3.29	1.86	2.15	4.16	5.30	2.09	4.73	0.45	2.42	0.01
56	ABHD14B	1.05	5.23	4.67	4.47	8.58	8.74	3.86	8.66	0.76	4.43	0.22
57	ABHD15	0.79	1.08	1.87	3.89	8.47	7.87	1.91	8.17	0.91	3.66	0.14
58	ABHD16A	0.43	4.18	3.64	3.68	4.09	5.67	2.98	4.88	0.79	2.88	0.11
59	ABHD17B	1.02	8.84	9.86	8.79	9.12	7.32	7.13	8.22	1.72	5.69	0.04
60	ABHD18	1.98	3.96	3.12	3.29	9.76	12.36	3.09	11.06	0.73	4.96	0.16
61	ABHD2	1.15	4.49	5.07	4.93	12.57	11.53	3.91	12.05	0.91	5.62	0.02
62	ABHD3	1.47	12.61	13.41	10.12	14.11	17.43	9.40	15.77	2.48	9.22	0.16
63	ABHD4	1.71	2.42	3.92	5.32	10.85	13.91	3.34	12.38	1.26	5.66	0.09
64	ABHD5	0.78	2.29	2.04	4.51	11.87	11.14	2.41	11.51	0.62	4.84	0.18
65	ABHD6	2.42	5.69	9.35	12.73	21.27	20.93	7.55	21.10	1.94	10.20	0.08
66	ABHD8	1.81	4.58	7.80	8.54	13.47	10.29	5.68	11.88	1.58	6.38	0.03
67	ABI1	0.77	6.11	4.26	5.58	3.63	6.78	4.18	5.21	1.11	3.50	0.04
68	ABI2	0.94	1.18	1.36	2.57	9.79	11.32	1.51	10.56	0.95	4.34	0.02
69	ABI3	1.57	12.29	13.36	9.09	15.50	16.43	9.08	15.97	2.23	9.09	0.14
70	ABI3BP	0.70	4.15	4.64	4.14	4.01	5.58	3.41	4.80	0.81	3.00	0.32
71	ABL1	1.52	2.70	1.81	3.54	14.44	16.21	2.39	15.32	1.36	6.36	0.09
72	ABL2	1.58	11.45	12.65	13.07	9.99	14.35	9.69	12.17	2.21	8.02	0.12
73	ABLIM1	0.61	4.73	3.95	3.68	4.46	5.27	3.24	4.87	0.74	2.95	0.15
74	ABLIM2	0.92	3.33	3.61	3.75	8.27	8.72	2.90	8.50	0.77	4.06	0.08
75	ABLIM3	0.97	3.17	6.22	6.55	9.09	9.52	4.23	9.31	0.79	4.77	0.05
76	ABRA	0.90	8.55	8.97	8.75	10.11	10.10	6.79	10.11	1.26	6.05	0.27
77	ABRAXAS2	1.71	2.20	1.70	4.59	17.48	14.65	2.55	16.07	1.24	6.62	0.08
78	ABTB1	0.41	0.67	0.53	2.47	6.60	8.72	1.02	7.66	0.55	3.07	0.07
79	ABTB2	0.86	7.53	8.54	7.32	6.44	10.65	6.06	8.55	1.22	5.28	0.03
80	ACAA2	0.87	9.17	8.91	7.73	8.31	12.08	6.67	10.20	1.45	6.10	0.27
81	ACAD10	1.59	8.65	7.70	7.67	13.72	15.87	6.40	14.80	1.19	7.46	0.31
82	ACAD8	1.51	1.52	2.37	3.84	8.69	11.28	2.31	9.98	0.94	4.41	0.22
83	ACAD9	2.98	6.05	4.18	4.54	21.52	23.80	4.44	22.66	1.35	9.48	0.27
84	ACADM	1.62	3.64	3.23	4.01	13.91	16.18	3.12	15.04	0.96	6.38	0.22
85	ACADS	1.01	6.60	5.63	6.70	7.82	9.51	4.98	8.66	1.08	4.91	0.04
86	ACADSB	1.06	1.04	0.96	2.09	8.26	9.71	1.29	8.98	0.52	3.60	0.29
87	ACADVL	0.29	1.13	0.67	1.26	2.41	2.73	0.84	2.57	0.22	1.21	0.26
88	ACAN	2.28	15.87	15.77	14.89	18.75	17.65	12.20	18.20	2.45	10.95	0.35
89	ACAP1	0.77	1.76	1.64	1.73	9.77	10.80	1.47	10.29	1.12	4.29	0.08
90	ACAP2	1.28	6.01	8.79	8.34	8.66	8.63	6.11	8.64	1.45	5.40	0.05
91	ACAT1	1.62	2.45	4.13	7.89	16.84	20.71	4.02	18.78	1.61	8.14	0.15
92	ACBD4	1.63	2.85	5.52	8.98	14.25	15.10	4.75	14.68	1.13	6.85	0.59
93	ACBD5	1.52	12.26	12.83	10.01	9.99	15.11	9.16	12.55	2.22	7.97	0.26
94	ACBD7	1.35	9.81	10.36	8.49	10.93	8.86	7.50	9.89	1.97	6.46	0.50
95	ACCS	1.50	3.58	3.98	4.51	19.50	21.65	3.40	20.57	1.36	8.44	0.24
96	ACD	0.32	0.13	0.34	0.65	2.84	3.42	0.36	3.13	0.25	1.25	0.52
97	ACE	0.96	4.18	8.66	6.43	11.66	13.57	5.06	12.62	1.21	6.30	0.11
98	ACE2	0.69	6.55	6.75	4.94	8.14	7.02	4.73	7.58	0.74	4.35	0.44
99	ACER1	1.46	9.95	10.37	9.62	13.57	16.03	7.85	14.80	2.06	8.24	0.17
100	ACER2	1.06	1.85	3.05	5.24	12.04	13.04	2.80	12.54	0.88	5.41	0.08