Table 3.
Identification of (A) significantly overrepresented cis-regulatory binding motifs in 5′ upstream regions and (B) significantly overrepresented promoter elements that bind known transcription factors (TF) or TF pairs according to ChiP-on-chip analysis (Harbison et al., 2004) in low-temperature up- and down-regulated gene clusters derived from C-Lim and N-Lim chemostat experiments
| (A) 5′ upstream cis-regulatory motif | ||||||
|---|---|---|---|---|---|---|
| Regulatory cluster | Motif name | Putative-binding protein | Promoter element | occa | Expected occb | occ Ec |
| Low Temperature C-lim Up | — | |||||
| Low Temperature C-lim Up | — | |||||
| Low Temperature N-lim Up | — | — | TGAAAAA | 206 | 113.04 | 2.30E-11 |
| PAC | — | CGATGAG | 57 | 17.49 | 6.1E-14 | |
| — | — | TGAGATG | 49 | 16.3 | 4.1E-07 | |
| Low Temperature N-lim Down | GATAA | Gln3/Gat1/Dal80/Gzf3 | AGATAAG | 203 | 102.57 | 3.1E-15 |
| STRE | Msn2/Msn4 | ACCCCTT | 29 | 8.73 | 1.6E-03 | |
| Low Temperature C- and N-lim Up | PAC | — | CGATGAG | 30 | 8.39 | 5.0E-05 |
| Low Temperature C- and N-lim Down | — | — | CGTCCAC | 13 | 2.85 | 7.8E-03 |
| (B) Overrepresentation of transcription factors (TF) binding targets | ||||||
|---|---|---|---|---|---|---|
| Regulatory cluster | Factor | p value | Kd | Fe | ||
| Low Temperature C-lim Up | Mbp1p | 1.6E-03 | 10 | 65 | ||
| Low Temperature C-lim Down | Hap2-Hap1 | 3.9E-05 | 3 | 4 | ||
| Hap3-Hap1 | 9.9E-06 | 3 | 3 | |||
| Low Temperature N-lim Up | Fhl1p | 3.4E-05 | 19 | 203 | ||
| Sfp1p | 1.3E-03 | 7 | 51 | |||
| Low Temperature N-lim Down | Gln3p | 2.1E-07 | 20 | 92 | ||
| Gln3-Dal82 | 5.5E-07 | 8 | 15 | |||
| Hap2-Dal82 | 6.8E-05 | 5 | 9 | |||
| Low Temperature C- and N-lim Up | ||||||
| Low Temperature C- and N-lim Down | Aft2p | 7.5E-04 | 10 | 34 | ||
| Hsf1p | 3.0E-08 | 16 | 133 | |||
| Nrg1p | 7.6E-07 | 14 | 128 | |||
| Phd1p | 3.3E-04 | 9 | 99 | |||
| Rcs1p | 1.1E-04 | 9 | 86 | |||
| Rox1p | 6.0E-05 | 8 | 62 | |||
| Sok2p | 5.7E-05 | 9 | 79 | |||
| Nrg1-Aft2 | 6.0E-05 | 5 | 20 | |||
| Phd1-Nrg1 | 1.4E-05 | 7 | 37 | |||
| Rox1-Phd1 | 7.8E-05 | 5 | 21 | |||
| Sok2-Nrg1 | 4.3E-07 | 8 | 33 | |||
(A) Significantly overrepresented cis-regulatory binding motifs in 5′ upstream regions. (B) Significantly overrepresented promoter elements that bind known transcription factors (TF) or TF pairs according to ChiP-on-chip analysis (Harbison et al., 2004). C-Lim, glucose-limited; N-Lim, ammonium-limited.
a The number of occurrences of promoter element in the regulatory cluster.
b Expected number of occurrences of the promoter element in a randomly chosen cluster of genes of the same cluster size.
c The probability of finding the number of patterns with the same level of overrepresentation, which would be expected by chance alone.
d Number of genes in category in cluster.
e Number of genes in category in genome.