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

Table 2 Mus musculus (embryonic stem cell) data

Data type	Data source	Notes
RNA-seq	[25]	18,936 genes RPKM-normalised [26]
TSS	Ensembl mm8/NCBIM36.46 [27]	Consider only most 5 ^′-located TSS for each gene
TF ChIP-seq	[21, 28]	E2f1, Esrrb, Klf4, c-Myc, n-Myc, Nanog, Oct4, Smad1, Sox2, Stat3, Tcfcp2l1 and Zfx
HM ChIP-seq	[29–31]	H3K4me1, H3K4me2, H3K4me3, H3K9me3, H4K20me3, H3K27me3 and H3K36me3
DNase-seq	[15, 32]	DNase I hypersensitivity
Gene ontology	[33, 34]	GOC validation date: 15 November 2013Structure from GO.db R package
Housekeeping annotations	[35]	3,689 orthologs inferred from the MGI human-mouse homology

Genes corresponding with haplotype variants, unmapped contig regions and low confidence RNA-seq mappings were removed, resulting in a set of 17,517 genes for analysis. Pre-processed RNA-seq and ChIP-seq data and mapped DNase I hypersensitivity in mESCs are available online [15, 32].
ChIP, chromatin immunoprecipitation; GOC, Gene Ontology Consortium; HM, histone modification; MGI, Mouse Genome Informatics; seq, sequencing; TF, transcription factor; TSS, transcription start site; RPKM, reads per kilobase per million.

ISSN: 1756-8935