Predicting expression: the complementary power of histone modification and transcription factor binding data

Table 3 Homo sapiens (GM12878 lymphoblastoid cell line) data

Data type	Data source	Notes
RNA-seq	ENCODE [59]	49,488 genesFPKM-normalised [60]
TSS	Ensembl hg19/GRCh37 [27]	Consider only most 5 ^′-located TSS for each gene
TF ChIP-seq	ENCODE [59]	c-Fos, Ctcf, Egr1, Nrf1, Nrsf, Pou2f2, Sp1, Srf, Stat3, Usf1 and Yy1
HM ChIP-seq	ENCODE [59]	H3K4me1, H3K4me2, H3K4me3, H4K20me1, H3K27me3 and H3K36me3
DNase-seq	ENCODE [59]	DNase I hypersensitivity
Gene ontology	[33, 34]	GOC validation date: 21 March 2014 Structure from GO.db R package
Housekeeping annotations	[61, 62]	3,804 genes Using RNA-seq data GSE30611

Genes corresponding with haplotype variants, unmapped contig regions and low confidence RNA-seq mappings were removed, resulting in a set of 38,041 genes for analysis.
ChIP, chromatin immunoprecipitation; GOC, Gene Ontology Consortium; HM, histone modification; seq, sequencing; TF, transcription factor; TSS, transcription start site.

ISSN: 1756-8935