CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes

Table 1 Summary of data sources integrated into CBS

Information	Source	Reference
D. melanogaster genome (BDGP R5/dm3)	UCSC Genome browser	[21]
D. melanogaster gene catalog	FlyBase	[36]
D. melanogaster gene catalog	RefSeq	[45]
D. melanogaster gene catalog	NCBI Entrez	[55]
Predictive models	JASPAR	[25]
Predictive models	TRANSFAC	[26]
H3K4Me1 ChIP-Seq profile	modENCODE	[35, 50]
H3K4Me3 ChIP-Seq profile	modENCODE	[35, 50]
H3K27Ac ChIP-Seq profile	modENCODE	[35, 50]
H3K27Me3 ChIP-Seq profile	modENCODE	[35, 50]
Conservation scores	UCSC Genome browser	[21]
Experimentally validated CRMs	REDfly	[39]
BLS predictions	BLS	[6]
D. ananassae genome	UCSC Genome browser	[21]
D. erecta genome	UCSC Genome browser	[21]
D. grimshawi genome	UCSC Genome browser	[21]
D. mojavensis genome	UCSC Genome browser	[21]
D. persimilis genome	UCSC Genome browser	[21]
D. pseudoobscura genome	UCSC Genome browser	[21]
D. sechelia genome	UCSC Genome browser	[21]
D. simulans genome	UCSC Genome browser	[21]
D. virilis genome	UCSC Genome browser	[21]
D. yakuba genome	UCSC Genome browser	[21]
Pairwise comparisons	UCSC / RefSeq	[21, 45]

ISSN: 1471-2164