Table 1.
List of 25 overrepresented motifs identified in this study
| Motif family | Motif number | Consensus motif pattern | Algorithms that identified the motifs | No. of clusters whose upstream sequences showed significant overrepresentation | ||
|---|---|---|---|---|---|---|
| |
|
5′ -> 3′ |
MEME |
AlignACE |
FIRE |
|
|
AP2_1-like |
Motif 1 |
BGCATGCAH |
+ |
+ |
+ |
33 |
| |
Motif 7 |
ACATGY |
- |
- |
+ |
6 |
| |
Motif 8 |
HTGCACH |
- |
- |
+ |
10 |
| |
Motif 11 |
MAMTGCA |
- |
- |
+ |
4 |
| |
Motif 23 |
DRMTTSCATB |
- |
- |
+ |
2 |
|
G-box-like |
Motif 2 |
DTGTGGGG |
+ |
+ |
+ |
38 |
| |
Motif 6 |
KKGRGGGGRR |
+ |
+ |
- |
16 |
|
E2F-like |
Motif 3 |
DTTGSCGCCH |
+ |
+ |
+ |
114 |
| |
Motif 4 |
TTTGGCGGGAAV |
+ |
+ |
- |
47 |
|
GAGA-like |
Motif 5 |
GDGRRRRARARRRARA |
+ |
+ |
- |
12 |
| |
Motif 13 |
WATTGCA |
- |
- |
+ |
6 |
|
CAAT-box-like |
Motif 16 |
TTTTGCM |
- |
- |
+ |
7 |
| |
Motif 20 |
BTAKTGCD |
- |
- |
+ |
8 |
| |
Motif 10 |
RMGACG |
- |
- |
+ |
1 |
|
Unknown set 1 |
Motif 12 |
GAGWCA |
- |
- |
+ |
5 |
| |
Motif 15 |
GAYCTMD |
- |
- |
+ |
9 |
| |
Motif 17 |
VYGTCBC |
- |
- |
+ |
1 |
| |
Motif 18 |
WTAGACR |
- |
- |
+ |
1 |
| |
Motif 19 |
HTAGVTCW |
- |
- |
+ |
1 |
| |
Motif 9 |
YTTACAT |
- |
- |
+ |
12 |
|
Unknown set 2 |
Motif 24 |
KATYTRCAH |
- |
- |
+ |
3 |
|
Other unknown |
Motif 14 |
MAACTA |
- |
- |
+ |
122 |
| |
Motif 21 |
VRTRAGGAD |
- |
- |
+ |
3 |
| |
Motif 22 |
HTKWYGAC |
- |
- |
+ |
5 |
| Motif 25 | WMTAANGA | - | - | + | 12 | |
IUPAC codes are used to represent each motif. The algorithm(s) that identified each motif are indicated, as well as the number of clusters containing the overrepresented upstream motif.