Is there a database of known transcription factor target genes for Solanum lycopersicum? Or a tool which can infer what genes accept which transcription factors in tomato?
I'm aware that the best way to classify this data is through CHiP-seq, but as for just initial manipulation with RNA-seq what are some good, plant based, transcription factor binding site programs to use?
1 answer
There are plenty of software for de novo motif discovery as well as comparison against known motifs. Meme-suit [http://meme-suite.org/] does it perfectly (MEME and DREME for de novo, and TOMTOM and Centrimo for comparison against known motifs). Jaspar [http://jaspar.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant/] has known motifs of plants that you can use as comparison while running Tomtom or Centrimo from Meme-suit.
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