Fig. 4

Integration of ChIP-seq and RNA-seq data to identify DEGs with differential H3K27me3 levels. A Venn diagram showing the overlap of DEGs from RNA-seq data and differential H3K27me3–associated genes from ChIP-seq data. A set of 150 genes in the overlapping regions were identified including 119 down-regulated DEGs with increased H3K27me3 levels and 31 up-regulated DEGs with decreased H3K27me3 levels. Significantly up- and down-regulated genes are highlighted in different colors according to log2^{(fold change)}. B Volcano plot showing the transcript levels of DEGs between FLHS and control hens. C Functional analysis of genes significantly changing in both up-regulated H3K27me3 modifications and gene expression. The rich factor is the ratio of the number of DEGs annotated in a given pathway to the total number of all genes annotated in the pathway. A higher rich factor indicates greater intensity. The size of the circle indicates the number of genes. D Representative genome tracks of RNA-seq and ChIP-seq data for SDC4 (syndecan 4). Y axis values show normalized read counts