Figure 1.

Groups of histone marks revealed by PCA. PCA of all ChIP-seq and MNase-seq data 10 kb up- and downstream of RefSeq TSSs is presented in a 3D stereoscopic image. Gray points represent the PCA loadings for each of the 41 histone marks and nucleosome occupancy (Nucs). Principal components (Comp.) 1, 2, and 3 are projected to the lower right, lower left, and top, respectively, with the orientation of the axes shown as gray bars radiating from the origin. Individual points representative of each component are colored: H3K4me3 (orange) for Comp. 1, Nucs (purple) for Comp. 2, and H3K79me2 (green) for Comp. 3. For reference, marks enriched at promoters are colored light orange and H3K36me3 is colored blue. Supplementary Figure 1 shows the fully labeled and separated PCA loadings and the transformed PCA scores plotted on the genome with respect to transcription start sites.