Confident gene activity prediction based on single histone modification H2BK5ac in human cell lines

Chitsazian, Fereshteh; Sadeghi, Mehdi; Elahi, Elahe

doi:10.1186/s12859-016-1418-6

BMC Bioinformatics

Table 3 Comparison of MDR and CART assessments of combinations of histone modifications for correlation with transcription

From: Confident gene activity prediction based on single histone modification H2BK5ac in human cell lines

Region	MDR: single^α	Tba^b	Root^c	Identity^d	MDR: 5 modifications^e	Tba^b	5 node tree^f	Identity^d
TSS-10	H3K79me1	0.6642	H3K79me1	+	2.20,4.91,3.27.3,3.79.1	0.719	3.27.3,2.20,3.79.1,4.91	100%
TSS-9	H3K79me1	0.6634	H3K79me1	+	2.20,3.27.3,3.79.2,3.79.1	0.7233	2.20,3.27.3,4.91,3.79.1	75%
TSS-8	H3K79me1	0.6717	H3K79me1	+	4.91,3.27.3,3.79.2,3.79.1	0.7327	3.27.3,2.20,3.79.1,4.91	75%
TSS-7	H2BK20ac	0.6686	H3K79me1	-	2.20,3.27.3,3.79.2,3.79.1	0.7368	3.27.3,2.20,3.79.1,3.79.2	100%
TSS-6	H2BK20ac	0.6856	H2BK120ac	-	2.20,2.5,3.27.3,3.79.1	0.7427	3.27.3,2.5,2.120,3.79.1	75%
TSS-5	H2BK120ac	0.7078	H2BK5ac	-	2.5,2.120,3.27.3,3.79.1	0.7638	3.27.3,3.79.1,2.120,2.5	100%
TSS-4	H2BK5ac	0.7252	H2BK5ac	+	2.5,4.91,3.27.3,3.79.1,	0.7761	2.5,3.27.3,2.20,4.8	50%
TSS-3	H2BK5ac	0.7673	H2BK5ac	+	2.5,2.120,3.79.1,3.79.2	0.7945	2.5,3.27.3,2.120,3.27.3	50%
TSS-2	H2BK5ac	0.7893	H2BK5ac	+	2.5,2.120,3.27,3.27.3	0.8093	2.5,2.120,3.27,2.9	75%
TSS-1	H2BK5ac	0.7903	H2BK5ac	+	2.5,3.27,4.91,3.79.2	0.8125	2.5,3.27.3,3.79.2,2.120	50%
TSS	H2BK5ac	0.7923	H2BK5ac	+	2.5,4.91,3.79.2,3.79.3	0.8181	2.5,3.79.2,4.91,3.79.3	100%
TSS+1	H4K91ac	0.6963	H2BK5ac	-	2.5,4.91,4.20.1,3.79.2	0.7322	2.5,3.27.3,3.36.3,4.20.1	50%
TTS	H4K20me1	0.6731	H4K20me1	+	3.27.1,3.27.3,3.36.3,4.20.1	0.7238	3.27.3,4.20.1,3.36.3,3.27.3	75%
TTS+1	H4K20me1	0.6757	H4K20me1	+	H2AZ,3.27.3,3.36.3,4.20.1	0.7239	H2AZ,3.27.3,4.20.1,3.36.3	100%
TTS+2	H4K20me1	0.6677	H4K20me1	+	4.91,3.27.3,2.5.1,4.20.1	0.6986	3.27.3,4.20.1,3.36.3,3.27.3	50%
TTS+3	H4K20me1	0.6673	H4K20me1	+	3.27.1,3.27.3,3.36.3,4.20.1	0.7133	2.5.1,3.27.3,4.20.1,3.27.3	50%
TTS+4	H4K20me1	0.6635	H4K20me1	+	3.27.1,3.36.3,3.27.3,4.20.1	0.7084	3.27.3,4.20.1,3.79.1,3.27.3	50%
TTS+5	H4K20me1	0.6617	H4K20me1	+	2.5.1,3.27.3,4.20.1,3.79.1	0.7088	3.27.3,4.20.1,3.79.1,3.27.3	75%

^α, MDR most informative single modification, ^b: Testing bal. accuracy ^c: Root of 5 node CART tree based on data presented in Fig. 3a, ^d: Identity between MDR & CART, ^eMDR: most informative combination of 5 modifications that are designated as described in legend to Fig. 3, ^f: Modifications in 5 node CART tree based on data presented in Fig. 3a

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