Fig. 3
Expression of genes regulated by cardiac-specific regulatory elements. A Scatterplot of pairwise comparison of the transcriptome of heart with brain, limb, and liver separately. Expression values are plotted as Log10(FPKM_avg). Category I genes are highlighted in pink. B Pie chart of the proportion of the genes in Category I that are expressed exclusively in the heart (pink) or in the heart and other tissues (green). C–E Left panel: genomic loci highlighting the CREs within the locus of 3 Category I genes (C Atp2a2, D Cbx5, and E Ppp1r3c) extracted from the UCSC genome browser [31]. Tracks from top to bottom are H3K4me1 marks for heart, brain, liver, and limb at E14.5—data sourced from ENCODE [21]. Histone peaks are marked in gray. Bold green dotted line represents the cardiac-specific promoter of the associated gene. Light green line marks the ubiquitous promoter. Right panel: in situ hybridization results of E14.5 mouse embryo—data from GXD [32]; lateral views, cranial to the top, front to the left. Related to Additional file 1: Fig S5