Arabidopsis Transcription Regulators

For generating the AtTR gene list, we started to collect information from major databases, websites, blast searches, and the latest research and review articles. To perform theses tasks, we used both manual procedures and Perl scripts. The Perl scripts are available upon request. In addition to the information from various publicly available databases, we collect and organize data from latest publications by copying gene lists directly from tables and/or figures. In case only a single or a few genes was/were reported, we performed Basic Local Alignment Search Tool (BlastP) search to find other possible members in the family using as query the amino acid sequence of either the motifs or the gene itself when no obvious motifs are present. All Blast searches were carried out online using TIGR's blast server, which runs WU BLAST 2.0 with default settings and TIGR's Arabidopsis protein database release 3.0. The blast results were manually examined to ensure accurate interpretation.


The list of TRs in a tab delimited format and a word document describing the procedures and resources used to collect the list can be downloaded here.

TR FAMILIES Number of members
MGH Mendel
AP2/EREBP 167 144
ABI3/VP1 14 14
Alfin-like 7 7
ARF (Auxin Response Factor) 24 23
Argonautea 10  
ARR-A class transcription factorb 11  
ARR-B class transcription factor, GARPb 12 12
Pseudo ARR transcription factorb 9  
G2-like transcription factor, GARPb 42 44
AS2/LOB (Asymmetric Leaves2/Lateral Organ Boundaries)c 43  
AT-rich interaction domain containing transcription factord 4  
AtSRe 7  
Aux/IAA 29 26
B3 transcription factorf 40  
bHLH (Basic Helix-Loop-Helix) 166 139
Bromodomain proteinsa 13  
bZIP transcription factor 95 81
BZR 6  
C2C2(Zn) CO-like, Constans-like zinc finger 35 33
C2C2(Zn) DOF zinc finger 40 37
C2C2(Zn) GATA transcription factor 29 28
C2C2(Zn) YABBY 6 6
C2H2 zinc finger 153 105
C3H zinc finger 143 33
CCAAT box binding factor    
unclassified CCAAT box binding factor 2  
DR1 2 2
HAP2 10 10
HAP3 11 11
HAP5 13 13
Chromatin remodeling factora, e 50  
CPP(Zn) (CPP1-related transcription factor) 8 8
Dicer-Like 4  
DNA methyltransferases 11  
E2F/DP transcription factor 9 8
EIN3 and EIN3-like(EIL) transcription factor 6 6
ELF3 and ELF3-likee 2  
FHAe 5  
GeBP and GeBP like 16  
General Transcription 91  
Global transcription factora 20  
GRAS transcription factor 32 32
HB (Homeobox transcription factor) 98 89
HMG (High mobility group)g 2 10
Histone acetyltransferase and Histone acetyltransferase related 14  
Histone deacetylases 18  
Histone 50  
HSF (heat shock transcription factor) 29 26
MADS box transcription factor 127 82
Methyl binding domain proteins 12  
MYB super family    
MYB domain transcription factor 184 136
MYB-related transcription factor 46 54
NAC domain transcription factor 116 109
NIN-like bZIP-related 14 15
Nucleosome/chromatin assembly factor (HMG homologs) a, g    
Nucleosome/chromatin assembly factor group A (NAP1 homologs) 6  
Nucleosome/chromatin assembly factor group B (CAF1 homologs) 2  
Nucleosome/chromatin assembly factor group C (RBP4/7 homolog) 5  
Nucleosome/chromatin assembly factor group D (HMG homologs) 12  
Nucleosome/chromatin assembly factor group E (ACF1 homologs) 1  
PHD finger transcription factor e, f 11  
PHOR1e 22  
Polycomb Group (PcG) Protein 13 4
Putative DNA-binding proteinf    
AT-hook DNA-binding protein 9  
pentatricopeptide (PPR) repeat-containing 10  
SAR DNA-binding protein 3  
DNA-binding protein 288  
Putative transcription regulatorf 89  
SBP (Squamosa promoter binding protein) 16 16
SET-domain transcriptional regulatora 39  
Silencing defectivea 2  
Silencing Groupa 5  
SNF7f 13  
TCP transcription factor 32 25
Trihelix (Triple-Helix transcription factor) 44 28
TUB transcription factor 11 11
WRKY domain transcription factorh 80 72
Zn-finger(CCHC) e 2  
PWWP doain proteine 4  
LUG and LUG-likee 2  
TAZ transcription factore 5  
NPR1 and NPR1-likee 6  
Other   20
Single Members    
COP1 1  
AN 1  
CIA2 1  
DET1 1  
EMF1 1  
FRY2 1  
LFY 1 1
MFP1 (MAR binding filament-like protein) 1  
RBL1 (Retinoblastoma) 1  
RHL1 1  
SAP 1  
SNI1 1  
SRS, SHI 1  
  2864 1533
Note: Family names used in Riechmann et al. (Science Vol. 290, 2105-2100, 15 December, 2000) were followed in most cases, which is available through TAIR. New families were added based on procedures described in the summary.
a. These families were obtained from ChromDB.
b. We did not follow the naming convention of the GARP super family. Rather we classified the genes to two families: ARR-B type and G2-like. However, two of the Pseudo ARR genes in our list were classified as GARP family members according to Mendel and Ohio State U AtTFDB. We believe this is why we have only 42 G2-like genes while Reichmann et al. reported 44.
c. AS2 and LOB are two different names for the same family of genes.
d. These families were extracted from the Mendel list made available through TAIR.
e. These families were obtained through literature search and/or blast.
f. These lists were obtained through TIGR gene name search and/or TAIR GO annotation filtering using relavant keywords.
g. There are totally 14 High mobility group (HMG) family genes, out of which 12 are also called "Nucleosome/chromatin assembly factor group D" in ChromDB. 3 of the 12 genes belong to the "ARID/BRIGHT" family according to TIGR ATH1 annotation. We classified these genes based on ChromDB. This is why there are only 2 HMG and no ARID/BRIGHT genes indicated in this table.
h. We couldn't find AGI number for WRKY5. The AGI number for AtWRKY33 is At2g38470. But BLASTN search using EST sequence AV526908 as query against TIGR ATH cDNA database revealed that WRKY73 might be the same as WRKY33.