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)