Table 1 |
||||
|
Overview of the TFBSs identified using co-expressed genes |
||||
| 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 |
YCYAACGGYYA |
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 |
|||
|
|
||||
|
*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. |
||||
|
Vandepoele et al. Genome Biology 2006 7:R103 doi:10.1186/gb-2006-7-11-r103 |
||||
