Choosing panels of genomics assays using submodular optimization

Table 2 Panels of histone modification assays chosen by SSA-future

Choice	Histone	Association	Singleton	Objective	Objective loss
order	modification		score	gain	if swapped in
1	H3K4me3	Promoters	3.18	3.18
2	H3K79me2	Transcription	2.40	0.97
3	H3K9me3	Constitutive heterochromatin	0.70	0.34
4	H3K27me3	Facultative heterochromatin	0.86	0.25
5	H3K36me3	Transcription	1.21	0.23
6	H3K4me1	Enhancers	1.86	0.18	0.05 (H3K36me3)
7	H3K4me2	Regulatory	3.12	0.08	0.07 (H3K36me3)
8	H3K9ac	Regulatory	3.13	0.07	0.15 (H3K36me3)
9	H2A.Z	Promoters	2.47	0.05	0.16 (H3K27me3)
10	H4K20me1	Transcription	1.41	0.005	0.22 (H3K36me3)
11	H3K27ac	Regulatory	2.61	0	0.14 (H3K36me3)

See the main text for a description of the “Objective loss if swapped in” column. There are only 11 histone modifications, so we display the full list. Bold font indicates those histone modification assays chosen by the Roadmap Epigenomics consortium

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