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Table 3 Numbers of putative transcription factor binding sites (TFBSs) and genes for the major transcription factor (TF) families in Arabidopsis, Brachypodium, wheat and barley. The TF families were sorted in descending order of the number of PWMs used in the TFBS prediction

From: Bioinformatic prediction of transcription factor binding sites at promoter regions of genes for photoperiod and vernalization responses in model and temperate cereal plants

TF familya No. PWMs No. TFBSs (genes)
Arabidopsis Brachypodium Wheat Barley
Myb/SANT 52 25 (15) 14 (8) 17 (15) 11 (10)
AP2 49 6 (5) 231 (28) 90 (44) 125 (33)
bHLH 30 39 (26) 1 (1) 10 (6) 17 (14)
bZIP 28 74 (43) 8 (6) 24 (21) 17 (13)
WRKY 27 3 (3) 0 (0) 2 (2) 1 (1)
HB 26 3 (3) 7 (7) 0 (0) 3 (3)
TCP 18 11 (8) 34 (17) 92 (37) 44 (16)
GATA 15 1 (1) 0 (0) 3 (2) 0 (0)
NAC/NAM 15 1 (1) 0 (0) 0 (0) 3 (3)
SBP 15 8 (8) 1 (1) 0 (0) 3 (3)
Dof 14 4 (4) 1 (1) 5 (5) 3 (3)
MADS box 12 469 (61) 513 (57) 673 (131) 251 (52)
AT hook 11 1 (0) 18 (14) 192 (100) 40 (23)
C2H2 ZF 11 0 (0) 3 (3) 0 (0) 13 (11)
CSD 1 374 (57) 76 (27) 308 (105) 115 (40)
  1. aThe full names of TF families are given in the “TF family names” tab of Additional file 3
  2. A brief functional annotation of these TF families is described below: Myb/SANT- Secondary metabolism, cellular morphogenesis, signal transduction in plant growth, abiotic and biotic stress responses, circadian rhythm, and dorsoventrality; AP2- Flower development, cell proliferation, secondary metabolism, abiotic and biotic stress responses, ABA response, and ethylene response; bHLH- Anthocyanin biosynthesis, light response, flower development and abiotic stress; bZIP- Seed-storage gene expression, photomorphogenesis, leaf development, flower development defense response, ABA response, and gibberellin biosynthesis; WRKY- Defense response HB (Homeodomain)- Development (leaf, root, internode, and ovule), stem cell identity, cell differentiation, growth responses, anthocyanin accumulation, and cell death; TCP- Flower development, asymmetry; GATA- Light response; NAC/NAM -Development, pattern formation, and organ separation; SBP- Plant development; Dof- Seed germination, endosperm-specific expression, and carbon metabolism; MADS box- Flower development, fruit development, flowering time, and root development; AT hook- Plant organ size and yield; CSD- Freezing tolerance, embryo development, flowering time, and fruit development; C2H2 ZF- Flower development, flowering time, seed development, and root nodule development