MARA - Motif Actitivity Response Analysis is a free online tool that recognizes most important transcription factors that are changing their activity in a set of samples.
The only input required is a set of microarray files. MARA normalizes them together, assigns PolII promoters and binding sites within them to probe sets present on the microarray, and runs the TF activity analysis. As a result MARA gives a PDF file with a sorted list of important TF, their activity changes across samples and a list of genes significantly regulated by them.
Currently eight human Affymetrix Gene Chips™ are supported: HG-U133A, HG-U133B and HG-U133+2, HG-U133A_2, HuGene-1_0-st-v1, HT_HG-U133A, HT_HG-U133B, HT_HG-U133_Plus_PM, and seven mouse chips MOE430A, MOE430B, Mouse430_2, Mouse430A_2, MoGene-1_0-st-v1, HT_MG-430A, HT_MG-430B. Please submit them one by one to online form, enter your email and press "Submit" button. You will receive email with links to results as soon as analysis is finished.
If you have more than 5 files please consider putting all .CEL files into archive (zip, tar.gz, tar.bz2) and submiting this archive to MARA. The archive should contain just .CEL files no folders or subfolders.