A general integrative genomic feature transcription factor binding site prediction method applied to analysis of USF1 binding in cardiovascular disease

Table 1 Description of the five genomic features used for USF1-BS prediction method development

Name	Description	Score range
PhastCons8^a,b	Conservation score across eight species (Human/chimp/mouse/rat/dog/chicken/fugu/zebrafish)	[-35,0]
MostCons8^a	Conserved region across eight species (Human/chimp/mouse/rat/dog/chicken/fugu/zebrafish)	[0, 1000]
RP5^a	Regulatory potential across five species (Human/chimp/mouse/rat/dog)	[-0.1, 0.9]
CpG^a,c	CpG island, CG dinucleotide-rich regions	[0.5, 1.6)
DNasel HS^d	Hypersensitive to DNaseI cleavage within human CD4⁺ cell	[0, 17)

^aDownloaded from the UCSC Genome Browser [19, 20].
^bBase-10 logarithm of the product of base-by-base conservation score within 10 base pair (bp) USF1-BS.
^cUsed centre position of 10 bp USF1-BS to define overlapping CpG island score.
^dPublished results [22].

ISSN: 1479-7364