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PlantRegMap/PlantTFDB v5.0
Plant Transcription
Factor Database
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Home TFext BLAST Prediction Download Help About Links PlantRegMap |
- The flowchart for construction of PlantTFDB
- Data source
- Data source (TFext)
- Pipeline to construct comprehensive protein dataset
- Family assignment rules
- List of studies which use the Family assignment rules
- Thresholds for domain identification
- Summary of TFs in different taxonomic lineages of green plants and the origination stage of TF families
- 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) | ||||
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) | |||
YABBY | YABBY (PF04690) | ||||
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) | ||||
GRAS | GRAS (PF03514) | ||||
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) | ||||
LFY | FLO_LFY (PF01698) | ||||
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-Y | NF-YA | CBFB_NFYA (PF02045) | |||
NF-YB | NF-YB (self-build) | ||||
NF-YC | NF-YC (self-build) | ||||
Nin-like | RWP-RK (PF02042) | ||||
NZZ/SPL | NOZZLE (PF08744) | ||||
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) | ||||
WRKY | WRKY (PF03106) | ||||
ZF-HD | ZF-HD_dimer (PF04770) |
- 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
![Family Schema](images/family_schema.jpg)
List of studies which use the Family assignment rules
Species | Common name | Authors | Journal | Year | PMID |
Ophiorrhiza pumila | - | Rai, A. et al. | Nat Commun | 2021 | 33452249 |
Syntrichia caninervis | - | Silva, A. T. et al. | Plant J | 2020 | 33277766 |
Brachypodium distachyon | stiff brome | Kouzai, Y. et al. | Plant J | 2020 | 32891065 |
Gossypium arboreum | tree cotton | Ashraf, J. et al. | BMC Genomics | 2020 | 32640982 |
Solanum lycopersicum | tomato | Keller, M. et al. | Sci Rep | 2020 | 32612181 |
Arachis hypogaea L. | peanut | Zhao, N. et al. | PLoS One | 2020 | 32271855 |
Chenopodium quinoa | quinoa | Wu, Q. et al. | Plant Physiol Biochem | 2020 | 32289638 |
Populus trichocarpa | black cottonwood | Chen, H. et al. | Plant Cell | 2019 | 30755461 |
Oryza sativa L. | rice | Kong, W. et al. | Plants (Basel) | 2019 | 30871082 |
Medicago truncatula | barrel medic | Sun, L. et al. | Plant J | 2019 | 30776165 |
Gossypium australe | - | Feng, S. et al. | BMC Plant Biol | 2019 | 31426739 |
Oryza glaberrima | African rice | Choi, J. Y. et al. | PLoS Genet | 2019 | 30845217 |
Glycine max | soybean | Gazara, R. K. et al. | Sci Rep | 2019 | 31270425 |
Trifolium pratense L. | red clover | Chao, Y. et al. | BMC Plant Biol | 2018 | 30477428 |
Arabidopsis pumila | - | Yang, L. et al. | BMC Genomics | 2018 | 30261913 |
Arachis ipaensis | - | Lu, Q. et al. | Front Plant Sci | 2018 | 29774047 |
Santalum album | white sandalwood | Mahesh, H. B. et al. | Plant Physiol | 2018 | 29440596 |
Foeniculum vulgare Mill. | fennel | Palumbo, F. et al. | Sci Rep | 2018 | 29993007 |