A Hypothesis-Based Approach
for Identifying the Binding Specificity of Regulatory Proteins
from Chromatin Immunoprecipitation Data

• Try it online
• View the Family Binding Profiles we derived for 36 DNA-binding domain families.
• Download the Family Binding Profiles in TAMO format.
• View the Restricted Family Binding Profiles we derived by excluding close homologs of the fourteen proteins in this study.
• Supplemental Tables for the paper.
• Supplemental Methods.
• Download the Restricted Family Binding Profiles.
• Raw Data from the ArrayExpress at EBI.
• Download all input sequences.  This includes:

• all bound sequences
• the complete set of sequences on each array
• the Markov background frequencies for each array

• The THEME algorithm has been integrated into our previously published motif analysis platform, TAMO and includes:

• The THEME engine and EM module
• Sample script for running THEME
• Sample THEME output
• DimerFinder code.

Contact Kenzie MacIsaacwith questions, comments or errors