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Table 1 Overview of the TFBSs identified using co-expressed genes

From: Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics

TFBS motif*

NCS†

Known motif

Site‡

Functional enrichment targets: GO Biological Process or Molecular Function§

nrCAAnTC (a)

5.77

BJ_CAAT-box

TGCAAATCT

GO:0008152 metabolism 8.58E-04 (1.2); GO:0003824 catalytic activity 8.91E-05 (1.2)

GTACAwry (b)

5.64

  

GO:0007275 development 2.89E-02 (1.6); GO:0003824 catalytic activity 2.98E-03 (1.2)

TTCkwwTs

5.79

BOXIINTPATPB

ATAGAA

 

sGCrGAGA

5.77

  

GO:0015980 energy derivation by oxidation of organic compounds 4.82E-02 (2.7); GO:0008152 metabolism 1.43E-03 (1.2); GO:0003824 catalytic activity 2.89E-03 (1.1)

kCCACGTn (4)

17.54

AT_G-box; HV_ABRE6; PH_boxII

GCCACGTGGA; GCCACGTACA; TCCACGTGGC

GO:0015979 photosynthesis 2.48E-04 (4.2); GO:0048316 seed development 2.64E-03 (3.6); GO:0009793 embryonic development (sensu Magnoliophyta) 6.15E-03 (3.5)

yCATTTnT (c)

8.7

GM_Unnamed_6

GCATTTTTATCA

GO:0003700 transcription factor activity 2.94E-03 (1.3); GO:0030528 transcription regulator activity 1.64E-02 (1.3); GO:0003677 DNA binding 3.86E-02 (1.2)

ynTTATCC

6.75

SREATMSD; AT_I-box

TTATCC; CCTTATCCT

 

nGTTGACw (d)

5.31

ZM_O2-site

GTTGACGTGA

GO:0006952 defense response 2.99E-04 (1.9); GO:0009607 response to biotic stimulus 3.56E-04 (1.7); GO:0016301 kinase activity 7.52E-11 (1.7)

TTTGCnrA

6.13

  

GO:0016773 phosphotransferase activity, alcohol group as acceptor 1.14E-02 (1.6); GO:0016772 transferase activity, transferring phosphorus-containing groups 2.60E-02 (1.5)

rATyTGGG

5.58

   

TrTwTATA

9.35

AT_TATA-box

TATATAA

GO:0019748 secondary metabolism 2.76E-02 (2.1); GO:0006519 amino acid and derivative metabolism 1.35E-02 (1.8); GO:0003700 transcription factor activity 3.36E-02 (1.3)

ATArwACA (e)

5.79

OS_Unnamed_2

CCATGTCATATT

 

nTTCCCGC (5)

27.27

NT_E2Fa

TTTCCCGC

GO:0006261 DNA-dependent DNA replication 6.48E-04 (6.2); GO:0000067 DNA replication and chromosome cycle 1.06E-07 (5.5); GO:0006260 DNA replication 3.57E-05 (5.1)

TkAGAwnA

8.86

BO_TCA-element3

TCAGAAGAGG

GO:0006464 protein modification 4.52E-02 (1.7); GO:0003824 catalytic activity 5.20E-03 (1.1)

AAACCCTA (13) (f)

40.06

TELOBOXATEEF1AA1

AAACCCTAA

Ribosome biogenesis and assembly 9.86E-13 (4.4); ribosome biogenesis 5.67E-12 (4.3); pre-mRNA splicing factor activity 3.20E-04 (3.9)

mGnyAAAG (g)

6.38

  

GO:0003824 catalytic activity 2.93E-02 (1.1)

GAnCnkmG

6.29

  

GO:0003729 mRNA binding 1.00E-02 (3.1); GO:0003735 structural constituent of ribosome 3.69E-02 (1.7); GO:0006412 protein biosynthesis 3.15E-03 (1.7)

TCnCTCTC

8.98

LE_5UTRPy-richstretch

TTTCTCTCTCTCTC

GO:0003777 microtubule motor activity 9.90E-03 (2.7); GO:0050789 regulation of biological process 2.27E-03 (1.4); GO:0016772 transferase activity, transferring phosphorus-containing groups 7.89E-03 (1.4)

wmGTCmAm

7.16

  

GO:0003824 catalytic activity 4.51E-03 (1.1)

ynCAACGG

8.39

CR_MSA-like

YCYAACGG YYA

GO:0003777 microtubule motor activity 3.17E-03 (3.4); GO:0003774 motor activity 8.55E-03 (2.9)

nmGATyCr

5.66

  

GO:0006944 membrane fusion 2.32E-02 (4.5); GO:0003735 structural constituent of ribosome 2.77E-03 (1.9); GO:0005198 structural molecule activity 7.11E-04 (1.9)

CGkCGmCn

7.68

OS_GC-motif5

CGGCGCCCT

 

AGGCCCAw (9)

21.94

UP1ATMSD

GGCCCAWWW

GO:0007046 ribosome biogenesis 3.56E-14 (4.3); GO:0042254 ribosome biogenesis and assembly 2.28E-14 (4.3); GO:0003735 structural constituent of ribosome 8.66E-29 (3.3)

AykyATwA

6.09

   

CTGnCTCy

6.91

  

GO:0016301 kinase activity 3.44E-02 (1.3); GO:0003676 nucleic acid binding 3.48E-02 (1.2); GO:0005488 binding 2.60E-03 (1.2)

TsTCGnTT

7.22

  

GO:0003824 catalytic activity 5.10E-03 (1.1)

TmAsTGAn

7.76

OS_GTCAdirectrepeat

TAAGTCATAACTGATGA

GO:0016491 oxidoreductase activity 3.85E-03 (1.5); GO:0008152 metabolism 5.74E-03 (1.2); GO:0003824 catalytic activity 5.70E-04 (1.2)

yyACrCGT (2)

6.56

ST_G-box

TCACACGTGGC

GO:0009605 response to external stimulus 4.80E-02 (1.6); GO:0006950 response to stress 3.42E-02 (1.6)

mATATTTT

5.51

GM_Nodule-site1

GATATATTAATATTTTATTTTATA

 

CCAATnCm

5.78

CAATBOX1; HV_ATC-motif

CAAT; GCCAATCC

GO:0008152 metabolism 2.01E-02 (1.2)

rkTCAwGm

5.42

  

GO:0003824 catalytic activity 6.17E-05 (1.2)

ssCGCCnA (2)

9.13

E2F1OSPCNA

GCGGGAAA

GO:0000067 DNA replication and chromosome cycle 4.74E-02 (3.0); GO:0006259 DNA metabolism 2.15E-03 (2.3); GO:0007049 cell cycle 4.29E-02 (2.2)

TTTATGnG

7.1

   

TCAwATAA

6.74

   
  1. *Numbers in parentheses indicate the number of clusters (containing co-expressed genes) in which the motif was independently identified. The letters in parenthesis refer to the updated TFBS identified using the two-way clustering: (a) GCAAnTCn; (b) GTACmwGy; (c) yCATTTAT; (d) mkTTGACT; (e) ATrrwACA; (f) AAACCCTA; (g) mGnCAAAG. †Network-level Conservation score. ‡Residues in bold indicate the matching position between the known motif and the motif found in this study. Known motifs were retrieved from PLACE [26] and PlantCARE [27]. §Only the first three GO categories according to the highest enrichment score are shown. The enrichment score is shown as number in parentheses.