Plant Transcription Factor Database
v4.0Previous version: v1.0, v2.0, v3.0
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- The flowchart for construction of PlantTFDB
- Data source
- Pipeline to construct comprehensive protein dataset
- Family assignment rules
- Thresholds for domain identification
- Pipeline for parsing BLAST reciprocal best hits (RBHs) and inferring orthologous groups
- Pipeline for GO annotation
- Curation and projection of TF binding motifs
- Transcription factor information
- Multiple sequence alignment
- Phylogenetic trees
- Quick search
- TF prediction server
- Help for PlantRegMap
Curation and projection of TF binding motifs
- 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.
- 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.
- 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).
- 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).
You can search for binding sites of TFs in promoter sequences using the binding site prediction server.