Supplementary Files

Title: "Chromatin properties of regulatory DNA probed by manipulation of transcription factors" by Sharov, A.A., Nishiyama, A., Qian, Y., Dudekula, D., Longo, D.L., Schlessinger, D., and Ko, M.S.H. submitted to the Journal of Computational Biology.

Supplementary Table S1. ChIP-seq data on binding of transcription factors and chromatin modifications in mouse ES cells
Supplementary Table S2. Corralation matrix between sets of z-values (to evaluate the association between the change of expression of target genes and presence of factors at transcription factor binding sites) obtained with 7 types of analysis.

Supplementary Table S3. Association between the response of target genes to manipulations of transcription factors (TFs) and presence of chromatin modifications and cofactors at TF binding sites.

Supplementary Table S4. Target genes regulated by transcription factors.