PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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)
RAV AP2 (PF00847)
B3 (PF02362)
B3 superfamily ARF B3 (PF02362) Auxin_resp (PF06507)
B3 B3 (PF02362)
BBR-BPC GAGA_bind (PF06217)
BES1 DUF822 (PF05687)
bHLH HLH (PF00010)
bZIP bZIP_1 (PF00170)
C2C2 CO-like zf-B_box (PF00643) CCT (PF06203)
Dof Zf-Dof (PF02701)
GATA GATA-zf (PF00320)
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)
CAMTA CG1 (PF03859)
CPP TCR (PF03638)
DBB zf-B_box (>=2) (PF00643)
E2F/DP E2F_TDP (PF02319)
EIL EIN3 (PF04873)
FAR1 FAR1 (PF03101)
GARP ARR-B G2-like (self-build) Response_reg (PF00072)
G2-like G2-like (self-build)
GeBP DUF573 (PF04504)
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)
HB-other homeobox (PF00046)
HRT-like HRT-like (self-build)
HSF HSF_dna_bind (PF00447)
LBD (AS2/LOB) DUF260 (PF03195)
MADS M_type SRF-TF (PF00319)
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)
NAC NAM (PF02365)
NF-X1 Zf-NF-X1 (PF01422)
NF-YB NF-YB (self-build)
NF-YC NF-YC (self-build)
Nin-like RWP-RK (PF02042)
S1Fa-like S1FA (PF04689)
SAP SAP (self-build)
SBP SBP (PF03110)
SRS DUF702 (PF05142)
STAT STAT (self-build)
TCP TCP (PF03634)
Trihelix Trihelix (self-build)
VOZ VOZ (self-build)
Whirly Whirly (PF08536)
ZF-HD ZF-HD_dimer (PF04770)
  1. 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.
  2. 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.
  3. Some C3H family proteins maybe not TF, some of them regulate RNA stability and some regulate RNA processing.
  4. 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
Family Schema

List of studies which use the Family assignment rules

SpeciesCommon nameAuthorsJournalYearPMID
Ophiorrhiza pumila-Rai, A. et al.Nat Commun202133452249
Syntrichia caninervis-Silva, A. T. et al.Plant J202033277766
Brachypodium distachyonstiff bromeKouzai, Y. et al.Plant J202032891065
Gossypium arboreumtree cottonAshraf, J. et al.BMC Genomics202032640982
Solanum lycopersicumtomatoKeller, M. et al.Sci Rep202032612181
Arachis hypogaea L.peanutZhao, N. et al.PLoS One202032271855
Chenopodium quinoaquinoaWu, Q. et al.Plant Physiol Biochem202032289638
Populus trichocarpablack cottonwoodChen, H. et al.Plant Cell201930755461
Oryza sativa L.riceKong, W. et al.Plants (Basel)201930871082
Medicago truncatulabarrel medicSun, L. et al.Plant J201930776165
Gossypium australe-Feng, S. et al.BMC Plant Biol201931426739
Oryza glaberrimaAfrican riceChoi, J. Y. et al.PLoS Genet201930845217
Glycine maxsoybeanGazara, R. K. et al.Sci Rep201931270425
Trifolium pratense cloverChao, Y. et al.BMC Plant Biol201830477428
Arabidopsis pumila-Yang, L. et al.BMC Genomics201830261913
Arachis ipaensis-Lu, Q. et al.Front Plant Sci201829774047
Santalum albumwhite sandalwoodMahesh, H. B. et al.Plant Physiol201829440596
Foeniculum vulgare Mill.fennelPalumbo, F. et al.Sci Rep201829993007
Only the representative publications since 2018 were listed.