TFdiff is a tool for identification of the (combination of) transcription factors (TFs) that are responsible for the differential expression of 2 sets of genes.
Click here for more details.
You can download a standalone version here (the TRANSFAC PWM-library is not included due to licensing reasons).

Input: 2 lists of RefSeq (NM_.*) and/or hugo ids (extracts promoter sequences of 800 bp upstream of the TSS) or 2 sequence files in fasta format (5'->3' orientation, only last 800 bp will be used)
Enter your first promoter set
by uploading a file:
 
by pasting in this box:
 
by selecting an example:
help
 
Group name:
Enter your second promoter set
by uploading a file:
 
by pasting in this box:
 
by selecting an example:
help
 
Group name:

Select a matrix dataset: help
Core and matrix similarity thresholds:
minimum False Negatives (only with TRANSFAC)
core 0.9 & matrix 0.75
core 1.0 & matrix 0.95
Background species:
Homo sapiens
Mus musculus
Xenopus tropicalis

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questions or comments: BioIT@IRC