Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data

Gong, Wuming; Koyano-Nakagawa, Naoko; Li, Tongbin; Garry, Daniel J

doi:10.1186/s12859-015-0460-0

Table 3 The 50 features based on ChIP-seq intensity of four histone marks (H3K27ac, H3K4me1, H3K4me3 and H3K27me3) and RNA polymerase II phosphorylation at serine 5 (RNAP)

From: Inferring dynamic gene regulatory networks in cardiac differentiation through the integration of multi-dimensional data

No.	Histone	Description	Dir.	P value	Signif.
20	H3K27ac	mean(x_t,1000)	+	4.40E-245	***
21		mean(x_t,500)	-	7.63E-03	**
22		mean(x_t,100)	-	1.59E-21	***
23		mean(x_t,50)	+	2.41E-06	***
24		mean(x_t,10)	-	2.09E-01
25		mean(x_t+1,1000)-mean(x_t,1000)	-	1.62E-04	***
26		mean(x_t+1,500)-mean(x_t,500)	-	9.25E-01
27		mean(x_t+1,100)-mean(x_t,100)	-	1.03E-03	**
28		mean(x_t+1,50)-mean(x_t,50)	+	6.40E-04	***
29		mean(x_t+1,10)-mean(x_t,10)	-	1.33E-01
30	H3K4me1	mean(x_t,1000)	+	9.27E-01
31		mean(x_t,500)	+	2.04E-07	***
32		mean(x_t,100)	+	1.04E-01
33		mean(x_t,50)	-	8.89E-01
34		mean(x_t,10)	-	3.06E-01
35		mean(x_t+1,1000)-mean(x_t,1000)	-	1.21E-56	***
36		mean(x_t+1,500)-mean(x_t,500)	+	2.42E-17	***
37		mean(x_t+1,100)-mean(x_t,100)	+	4.97E-05	***
38		mean(x_t+1,50)-mean(x_t,50)	-	4.04E-01
39		mean(x_t+1,10)-mean(x_t,10)	+	8.39E-01
40	H3K4me3	mean(x_t,1000)	-	3.34E-91	***
41		mean(x_t,500)	+	2.34E-32	***
42		mean(x_t,100)	+	1.28E-02	*
43		mean(x_t,50)	-	8.41E-01
44		mean(x_t,10)	+	7.33E-01
45		mean(x_t+1,1000)-mean(x_t,1000)	-	3.73E-23	***
46		mean(x_t+1,500)-mean(x_t,500)	+	3.82E-01
47		mean(x_t+1,100)-mean(x_t,100)	+	3.15E-04	***
48		mean(x_t+1,50)-mean(x_t,50)	+	9.68E-01
49		mean(x_t+1,10)-mean(x_t,10)	-	7.65E-01
50	H3K27me3	mean(x_t,1000)	+	1.61E-15	***
51		mean(x_t,500)	-	1.83E-27	***
52		mean(x_t,100)	+	7.01E-02
53		mean(x_t,50)	-	2.04E-01
54		mean(x_t,10)	-	8.98E-02
55		mean(x_t+1,1000)-mean(x_t,1000)	+	1.77E-08	***
56		mean(x_t+1,500)-mean(x_t,500)	-	9.39E-05	***
57		mean(x_t+1,100)-mean(x_t,100)	+	2.15E-01
58		mean(x_t+1,50)-mean(x_t,50)	-	3.05E-01
59		mean(x_t+1,10)-mean(x_t,10)	-	4.10E-01
60	RNAP	mean(x_t,1000)	-	0.00E + 00	***
61		mean(x_t,500)	+	1.82E-105	***
62		mean(x_t,100)	+	1.04E-13	***
63		mean(x_t,50)	-	1.54E-01
64		mean(x_t,10)	+	9.46E-01
65		mean(x_t+1,1000)-mean(x_t,1000)	-	6.44E-166	***
66		mean(x_t+1,500)-mean(x_t,500)	+	1.98E-31	***
67		mean(x_t+1,100)-mean(x_t,100)	+	5.17E-03	**
68		mean(x_t+1,50)-mean(x_t,50)	-	4.77E-01
69		mean(x_t+1,10)-mean(x_t,10)	+	1.96E-01

*: 0.01 ≤p value < 0.05; **: 0.001≤p value < 0.01; ***: p value < 0.001.

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