Choosing panels of genomics assays using submodular optimization

Table 1 Panels of transcription factors assays chosen by SSA-future

Choice	Transcription factor	Function	Singleton	Objective
order			score	gain
1	SMARCB1	ATP-dependent chromatin remodeling	14.78	14.78
2	PML	Tumor suppression	14.12	1.84
3	STAT5A	Developmental signal transduction	14.17	0.91
4	CTCF	Chromatin conformation and insulation	8.40	0.81
5	BRF2	RNA polymerase III initiation complex	8.88	0.55

Each list is in the order assigned by SSA; for any size k, the top k assay types in the list are the chosen panel of this size. The “singleton score” is the objective value of a panel containing only the indicated assay type, and the “objective gain” indicates the improvement in the objective that results from SSA adding the indicated assay type to the growing panel. Because there are 80 transcription factors, we display just the top five chosen by SSA. Associations are summarized from UniProt [22]
SSA submodular selection of assays

ISSN: 1474-760X