Plant Transcription Factor Database
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Curation and projection of TF binding motifs

Curation and projection of TF binding motifs

  1. Firstly, we collected binding motifs derived from experiments from PlantCistromeDB, CIS-BP, JASPAR, UniPROBE, TRANSFAC (public 7.0), literature and motifs discovered from ChIP-seq peaks using MEME-ChIP.
  2. For TFs with more than one motif, we manually selected the best one preferentially for the motif determined in vivo and presenting more similarity with other motifs of this TF.
  3. Filtered out low-quality ones (these with information content less than 4.5), and got 674 non-redundant, high-quality binding motifs (Motif information, All motifs in one file, and Individual motifs).
  4. Projected the set of motifs to other species using the RBHs in the same family, and adjusted the motifs using the nucleic acid background in promoter regions (TSS -500bp to +100bp).
Finally, we got sets of species-specific binding motifs for 156 species. The binding motifs of TFs can be viewed at the information page of corresponding TFs, or download them here.

You can search for binding sites of TFs in promoter sequences using the binding site prediction server.