Additional data file 1:

Figure S1: distribution of C+G and CG dinucleotide fractions in the ± 100-bp region flanking the three classes of CTCF sites. Figure S2: distributions of distances from a repeat for each of the three CTCF classes. Figure S3: distributions of differences in gene expression for gene pairs within CTCF blocks. Figure S4: expression distribution for the gene closest to a CTCF site for each of the three classes. Figure S5: distributions of mouse CTCF sites in the three classes. Table S1: class versus class comparison of densities of various histone marks in the 500-bp region flanking CTCF sites. Table S2: fraction of sites within each CTCF site class with unequal distributions of a specific histone mark in upstream and downstream regions (± 5 kbp). Table S3: comparison of upstream and downstream tag counts of various histone marks for each class of CTCF site. Table S4: class versus class comparison of tag-density-differential for various histone marks. Table S5: motifs enriched in the 200-bp flanking region of bound CTCF sites. Table S6:functional enrichment near each of the three CTCF site classes. Table S7: tendency of functional categories enriched near CTCF site classes to have higher or lower expression than background genes. Tables S8: k-mers enriched in each of the three classes of sites relative to the other two classes. Table S9: summary of the main observed differences between the three classes of site.

Format: DOC Size: 364KB Download file

This file can be viewed with: Microsoft Word Viewer

Additional data file 2:

Coordinates of the CTCF sites shared among the four cell types.

Format: TXT Size: 219KB Download file

Additional data file 3:

Experimentally determined CTCF sites in human and mouse and their occupancy classes.

Format: DOC Size: 291KB Download file

This file can be viewed with: Microsoft Word Viewer