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
Family Assignment Rules
After a systematically reviewing recently-published literatures, we refined family assignment rules. Families that do not meet the criteria ('Transcription factors are proteins that show sequence-specific DNA binding and are capable of activating or/and repressing transcription') were excluded in the updated version, such as transcription cofactors (e.g. AUX/IAA, GIF and chromatin related proteins like chromatin remodeling factors (e.g. ARID), histone demethylases (e.g. JUMONJI), histone acetyltransferase (e.g. PcG ). Moreover, questionable families (e.g. TUBBY-like, Alfin-like, FHA, and ZIM) were also removed in the updated PlantTFDB. On the other side, five newly identified TF families (DBB, FAR1, LSD, NF-X1, STAT) were added. Considering differences in domain composition, DNA binding specificity and function, AP2/ERF and HB families in previous PlantTFDB were divided to sub-families. Especially, because it has been reported that some M type MADS could be potential pseudogenes or a new class of transposable elements, we also subdivided those M type MADS to a new subfamily.
In new rules, there were three types of domain to determine which family a TF belongs to, including DNA-binding domain, auxiliary domain and forbidden domain. In most cases, DNA-binding domain self can assign a TF to one certain family correctly. But In some cases, an auxiliary domain was needed to classify TF into corresponding family. For example, if a protein only contains a DNA-binding domain - B3, we can assign it to B3 superfamily. However, B3 superfamily can be divided into two subfamilies (ARF and B3), and so auxiliary domain need be used to distinguish these two families: if the protein contains Auxin_resp domain, it was assigned to ARF family, else it will be assigned to B3 family. Different from previous version, forbidden domains were used to distinguish proteins containing DNA-binding domain but having no transcription activity. If a protein contains the forbidden domain, then we think it was not TF, and should not be collected by PlantTFDB.
Table of family assignment
|Family||DNA-binding domain||Auxiliary domain||Forbidden domain|
|AP2/ERF||AP2||AP2 (>=2) (PF00847)|
|ERF||AP2 (1) (PF00847)|
|B3 superfamily||ARF||B3 (PF02362)||Auxin_resp (PF06507)|
|C2C2||CO-like||zf-B_box (PF00643)||CCT (PF06203)|
|LSD||Zf-LSD1 (PF06943)||Peptidase_C14 (PF00656)|
|C2H2||zf-C2H2 (PF00096)||RNase_T (PF00929)|
|C3H||Zf-CCCH (PF00642)||RRM_1 (PF00076) or Helicase_C (PF00271)|
|DBB||zf-B_box (>=2) (PF00643)|
|GARP||ARR-B||G2-like (self-build)||Response_reg (PF00072)|
|GRF||WRC (PF08879)||QLQ (PF08880)|
|HB||HD-ZIP||Homeobox (PF00046)||HD-ZIP_I/II (self-build) or SMART (PF01852)|
|TALE||Homeobox (PF00046)||BELL (self-build)or ELK (PF03789)|
|WOX||homeobox (PF00046)||Wus type homeobox (self-build)|
|HB-PHD||homeobox (PF00046)||PHD (PF00628)|
|LBD (AS2/LOB)||DUF260 (PF03195)|
|MIKC||SRF-TF (PF00319)||K-box (PF01486)|
|MYB superfamily||MYB||Myb_dna_bind (>=2) (PF00249)||SWIRM (PF04433)|
|MYB_related||Myb_dna_bind (1) (PF00249)||SWIRM (PF04433)|
- Some proteins containing just one AP2 domain are distinct from proteins from ERF family and more closely related to AP2 family. Those proteins are assignment to AP2 family. Two self-build models are used to distinguish those proteins from ERF proteins.
- Only a subset of C2H2 zinc-finger containing proteins are real TF, many of them maybe not TF and act in RNA metabolism and chromatin-remodeling.
- Some C3H family proteins maybe not TF, some of them regulate RNA stability and some regulate RNA processing.
- ZF-HD_dimer is not DBD but the region involved in the formation of homo and heterodimers. To keep consistent with other rules, we classify it to DBD.
Schema of family assignment