Different transcriptional analysis tools give different enrichment of TFs - (Dec/21/2014 )

Hi everyone,

when I check for TF-binding sites in a list of genes/RefSeq identifiers, I have the problem that depending on which tools I use (for instance GATHER gather.genome.duke.edu or TFM-Explorer http://bioinfo.lifl.fr/TFM/TFME/), I get enrichment for completely different TFs. I also set up a trial account with the commercial Genomatix - MatInpector, and I got yet another completetly different TFs !

Unfortunately, I don't know a lot about bioinformatics, so I'd really appreciate some help. I do know that some tools use the TRANSFAC library vs the JASPAR library and that the free version of the TRANSFAC again differs from the commercial one etc. But should the two versions of TRANSFAC for example really differ that much and which results should I trust ?

I feel bad about trying to conclude someting when the variability between different analyses is like 100%, so I'm at a loss what to do... ?

Does no-one have an idea ?   I'm really baffled at this...