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Table 2 Regulated transcription factors during CIM and SIM

From: Genome scale transcriptome analysis of shoot organogenesis in Populus

   NO. NO. B vs. A C vs. A D vs. A E vs. A
Gene family Percentage (regulated) (total) Up Down Up Down Up Down Up Down
SRS 80.0% 8 10 3   5   2   4  
TLP 72.7% 8 11   6 4 4 2 6 2 4
AUX-IAA 69.7% 23 33 9 11 2 16   27   15
CCAAT-HAP2 45.5% 5 11   5   2   4   4
GRF 44.4% 4 9        4  
C2C2-Dof 42.9% 18 42 5 11   13 3 13   14
WRKY 38.5% 40 104 22 12 27 14 29 14 25 10
ARF 37.8% 14 37   13   10   13   10
HB 37.7% 40 106 15 23 7 22 7 24 6 24
AS2 36.8% 21 57 8 4 15 2 8 4 6 3
FHA 36.8% 7 19   7   8   4   4
ZIM 36.4% 8 22 8 3 7 2 5 3 4 2
GARP-G2-like 35.8% 24 67 2 19 4 14 6 19 3 15
TCP 35.3% 12 34   11 2 9   9 3 8
HMG 33.3% 4 12 2 2 2 2 2 3 2 3
LIM 33.3% 7 21   7   7   7   7
ULT 33.3% 1 3    1   1   1  
ZF-HD 32.0% 8 25   6   4   3 2  
E2F-DP 30.0% 3 10 2 2       
SBP 27.6% 8 29   8 4 5   7   6
CCAAT-HAP3 26.3% 5 19   5   3   3   3
Trihelix 25.5% 12 47 4 6 4 4 5 4 4 3
bHLH 25.0% 37 148 9 25 5 27 5 24 4 19
PLATZ 25.0% 5 20 5 4 4 2 3 2 3 2
bZIP 22.4% 19 85 4 22 2 18 4 17 3 17
Alfin 22.2% 2 9   2       
GRAS 20.8% 20 96 7 12 5 7 8 12 5 7
MYB-related 20.2% 17 84 5 14 3 6 2 7 2 6
HSF 19.4% 6 31 7   11   7   5  
MYB 19.0% 41 216 13 27 11 27 12 29 11 27
AP2-EREBP 18.9% 40 212 28 10 23 8 25 8 25  
NAC 18.6% 32 172 16 15 10 13 6 15 7 13
C2C2-CO-like 17.9% 7 39   10   6   7   5
C3H 17.9% 14 78 10 3 9 2 7 5 6 2
PcG 17.8% 8 45 2 6 2 3   3   2
C2H2 16.0% 13 81 5 11 3 9 3 9 2 9
C2C2-GATA 15.6% 5 32   2   2 3 3   
C2C2-YABBY 15.4% 2 13        3  
JUMONJI 15.0% 3 20      2    
TAZ 14.3% 1 7     1   1   
GARP-ARR-B 13.3% 2 15   4    2 3   3
ABI3-VP1 11.1% 12 108 9 4 9 2 10 2 9 6
MADS 10.8% 12 111   8 2 7 6 5 2 6
CCAAT-HAP5 10.5% 2 19      2   2  
PHD 9.3% 8 86 7 3 5   3 2 4 2
Total 22.8% 588 2576         
  1. The JGI gene model IDs were downloaded from the Database of Poplar Transcription Factors (DPTF) and were searched against the list of the differentially expressed genes identified by LIMMA. The list is ranked by the percentage of the total number of each transcription factor class in poplar. The total number of regulated transcription factors were corrected for redundancy among the array probes; the number of up-or down-regulated transcription factors at each stage were not corrected for redundancy (i.e., multiple probe sets targeting the same transcript may be present).