Table 2.

Over-Represented Transcription Factor Motifs Within the 5′ Regions Upstream of Cell Cycle Gene Cluster Gene Transcription Start Sites

Clover: Cis-eLement OVERrepresentation
Motif file: JASPAR2005_CORE (123 motifs)
Over- and under-represented motifs:
Motif	Raw score	p-value from randomizing
MA0015 CF2-II ZN-FINGER, C2H2	101	0.006
MA0060 NF-Y CAAT-BOX	92.9	0.002
MA0049 Hunchback ZN-FINGER, C2H2	56	0.992
MA0031 FOXD1 FORKHEAD	38.2	0.001
MA0091 TAL1-TCF3 bHLH	33.1	0
MA0111 Spz1 bHLH-ZIP	29.3	0.001
MA0024 E2F1 Unknown	22.3	0
MA0033 FOXL1 FORKHEAD	7.21	0.001

Clover program identified the enriched motifs within the 5 kb 5′ regions upstream of CCGC gene transcription start sites, using all 5 kb 5′ regions of the transcription start sites of all known zebrafish genes as a background control. Statistical significance of a given motif in a set of regulatory sequences is described as p, with a value<0.01 indicating the significance of enrichment of this motif in these target sequences.

CCGC, cell cycle gene cluster.