Table II.
Occurrence of CBS, EE, G-Box, and Hex elements in predicted Arabidopsis promoters
Expected values were determined by establishing the frequency of the oligonucleotide in the 25,545 random Arabidopsis promoters. Gene sets are defined as follows: Harmer Circadian, genes defined as circadian regulated in continuous light by Harmer et al. (2000); Schaffer Circadian, genes defined as circadian regulated in continuous light by Schaffer et al. (2001); Schaffer Light Induced, the subset of circadian genes defined Schaffer et al. (2001) in which expression was higher in the day than in the night; Schaffer Dark Induced, the subset of circadian genes defined Schaffer et al. (2001) in which expression was higher in the night than in the day; Schaffer Diurnal, genes shown to oscillate in a light-dark cycle by Schaffer et al. (2001).
| Arabidopsis Genome
|
Affymetrix Gene Chip
|
AFCG Chip
|
||||||||
| Motif | 8mer | Observed % (#) | Expected % (#) | Obs/exp | Observed % (#) | Expected % (#) | Obs/exp | Observed % (#) | Expected % (#) | Obs/exp |
| CBS | AAAAATCT | 35 (9035) | 53 (13641) | 0.66 | 36 (2602) | 53 (3798) | 0.69 | 35 (2468) | 53 (3692) | 0.67 |
| EE | AAATATCT | 25 (6455) | 35 (9042) | 0.71 | 25 (1825) | 35 (2508) | 0.73 | 26 (1840) | 35 (2508) | 0.73 |
| G-Box | CCACGTGG | 3 (651) | 1 (332) | 1.96 | 3 (188) | 1 (71) | 2.64 | 3 (188) | 1 (71) | 2.64 |
| Hex | TGACGTGG | 5 (1274) | 3 (817) | 1.56 | 6 (406) | 3 (214) | 1.89 | 6 (389) | 3 (214) | 1.80 |
| Total Genes | 25,545 | Total Genes | 7,166 | Total Genes | 6,966 | |||||
|
CCG-ET
|
Harmer Circadian
|
Schaffer Circadian
|
||||||||
| Motif | 8mer | Observed % (#) | Expected % (#) | Obs/exp | Observed % (#) | Expected % (#) | Obs/exp | Observed % (#) | Expected % (#) | Obs/exp |
| CBS | AAAAATCT | 35 (8) | 53 (12) | 0.66 | 39 (153) | 53 (204) | 0.75 | 40 (64) | 53 (85) | 0.75 |
| EE | AAATATCT | 22 (5) | 35 (8) | 0.62 | 37 (145) | 35 (135) | 1.07 | 43 (69) | 35 (56) | 1.23 |
| G-Box | CCACGTGG | 4 (1) | 1 (0.23) | 4.35 | 4 (17) | 1 (4) | 4.25 | 7 (11) | 1 (2) | 5.50 |
| Hex | TGACGTGG | 4 (1) | 3 (0.69) | 1.45 | 8 (30) | 3 (12) | 2.50 | 10 (10) | 3 (5) | 2.00 |
| Total Genes | 23 | Total Genes | 386 | Total Genes | 161 | |||||
| Schaffer Light Induced
|
Schaffer Dark Induced
|
Schaffer Diurnal
|
||||||||
| Motif | 8mer | Observed % (#) | Expected % (#) | Obs/exp | Observed % (#) | Expected % (#) | Obs/exp | Observed % (#) | Expected % (#) | Obs/exp |
| CBS | AAAAATCT | 34 (32) | 53 (50) | 0.64 | 38 (199) | 53 (280) | 0.71 | 41 (276) | 53 (354) | 0.80 |
| EE | AAATATCT | 27 (25) | 35 (33) | 0.75 | 37 (198) | 35 (185) | 1.07 | 38 (254) | 35 (234) | 1.08 |
| G-Box | CCACGTGG | 9 (8) | 1 (0.93) | 8.60 | 5 (27) | 10 (53) | 0.50 | 4 (27) | 1 (7) | 3.85 |
| Hex | TGACGTGG | 8 (7) | 3 (3) | 2.33 | 8 (41) | 3 (16) | 2.56 | 9 (57) | 3 (20) | 2.85 |
| Total Genes | 93 | Total Genes | 530 | Total Genes | 668 | |||||
| Harmer % (rhythmic with motif/total genes with motif)
|
Schaffer % (rhythmic with motif/total genes with motif)
|
|||||||||
| Motif
|
8mer
|
1 copy
|
2 copies
|
3 or more
|
1 copy
|
2 copies
|
3 or more
|
|||
| CBS | AAAAATCT | 6 (119/1991) | 6 (28/483) | 5 (6/128) | 3 (47/1897) | 4 (15/437) | 2 (2/134) | |||
| EE | AAATATCT | 6 (96/1493) | 12 (32/278) | 32 (17/54) | 3 (44/1493) | 6 (17/278) | 13 (8/62) | |||