Additional file 1: of Functional annotation of the cattle genome through systematic discovery and characterization of chromatin states and butyrate-induced variations

Figure S1. General characteristics for 38 epigenomic data sets. Figure S2. Distribution of peak-length for all 38 epigenomic data sets. Figure S3. Distribution of distances between peaks and their nearest genes for all 38 epigenomic data sets. Figure S4. Correlations of peak-length vs. chromosome-length for all 38 epigenomic data sets. Figure S5. Correlations of peak-length vs. gene-length for all 38 epigenomic data sets. Figure S6. Correlations of peak-length vs. exon-length for all 38 epigenomic data sets. Figure S7. Correlations of epigenomic, RNA-seq, and DNA methylation data sets. Figure S8. Genes specifically highly expressed (n = 1230; top 5%) in rumen epithelial primary cells (REPC). Figure S9. Gene-length distribution across the four gene sets. Figure S10. The dn/ds ratio comparison for the four gene sets corresponding to orthologous genes across mammals. Figure S11. The expression levels of the four orthologous gene sets in 53 human tissues. Figure S12. The expression levels of the four orthologous gene sets across 159 mouse tissues. Figure S13. The expression levels of the four orthologous gene sets in 174 sheep tissues. Figure S14. Functional enrichment analysis for the four gene sets. Figure S15. Enrichment of chromatin states for differentially methylated regions induced by butyrate treatment in rumen epithelial primary cells (REPC). Figure S16. Butyrate-induced dynamics in chromatin states and gene expression. Figure S17. Associations of downregulated differentially expressed genes (down-DEGs) with alterations of chromatin states. (DOCX 6756 kb)