|
Enrichment of transcription factors (TF) binding in clusters of genes that were differentially expressed in response to fully fermentative conditions. Clusters A & B, 2 & 3 and 4, 5 & 6 had similar expression pattern and similar enrichments, thereby these were analyzed together. Enrichment of TF binding according to the dataset of Harbison et al. [57] was given in p-value. Specific TF binding sites not present in the Harbison dataset (PAC, RRPE and Upc2p) were analyzed by using web-based software RSAT http://rsat.ulb.ac.be/rsat/ and indicated in italics. |
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| Transcription factor |
A&B |
C |
D |
||||||
| Name |
clustera |
binding motif |
nr of genesb |
nr of genesc |
enrichmentd |
nr of genesc |
p-value |
nr of genesc |
enrichmentd |
|
|
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| Met32p |
B |
AAACTGTGG |
22 |
6 |
2.94E-04 |
||||
| Gcn4p |
NC |
TGAsTCA |
192 |
22 |
3.54E-05 |
20 |
2.54E-05 |
||
| Bas1p |
NC |
TGACTC |
36 |
14 |
1.19E-11 |
||||
| Rap1p |
NC |
CAyCCrTrCA |
157 |
49 |
2.79E-33 |
||||
| Sfp1p |
NC |
AyCCrTACAy |
51 |
25 |
5.25E-23 |
||||
| Fhl1p |
NC |
TGTAyGGrTG |
203 |
72 |
3.54E-54 |
||||
| Gln3p |
NC |
GATAAGa |
92 |
7 |
2.35E-04 |
||||
|
|
|||||||||
| PAC |
- |
wGmGATGAGv [22] |
376 |
98 |
5.7 |
||||
| RRPE |
- |
TGAAAAwTTT [22] |
535 |
110 |
4.2 |
||||
| Upc2p |
NC |
TCGTwhAG [42] |
667 |
16 |
1.7 |
||||
|
|
|||||||||
| Transcription factor |
1 |
2&3 |
4,5&6 |
||||||
| Name |
clustera |
binding motif |
nr of genesb |
nr of genesc |
p-value |
nr of genesc |
p-value |
nr of genesc |
enrichmentd |
|
|
|||||||||
| Nrg1p |
NC |
GGaCCCT |
128 |
25 |
1.59E-04 |
||||
| Hap1p |
NC |
GGnnATAnCGs |
73 |
25 |
1.75E-09 |
||||
| Msn2p |
5 |
mAGGGGsGG |
65 |
20 |
5.57E-07 |
||||
| Sut1p |
A |
GCsGsGnnsG |
50 |
17 |
8.21E-07 |
||||
| Skn7p |
NC |
GnCnnGsCs |
156 |
37 |
2.56E-08 |
||||
| Msn4p |
5 |
mAGGGG |
56 |
18 |
1.00E-06 |
||||
| Hsf1p |
NC |
TTCynnnnnnTTC |
133 |
31 |
5.38E-07 |
||||
| Hap4p |
3 |
GnCcAAtcA |
54 |
16 |
1.31E-05 |
||||
| Ash1p |
NC |
yTGACT |
20 |
7 |
1.29E-03 |
||||
| Sok2p |
NC |
TGCAGnnA |
79 |
20 |
1.55E-05 |
||||
| Ume6p |
NC |
TAGCCGCCsA |
132 |
28 |
1.33E-05 |
||||
| Rpn4p |
3 |
GGTGGCAAA |
93 |
21 |
1.60E-04 |
||||
| Mbp1p |
NC |
ACGCGT |
165 |
44 |
1.75E-10 |
||||
| Swi6p |
NC |
CGCGAAAA |
140 |
27 |
3.32E-04 |
||||
|
a: presence of the transcription factor in one of the clusters; NC = transcription factor not significant changed over time b: amount of genes in the genome belonging to the specified transcription factor c: amount of genes in the respective clusters or group of clusters belonging to the specified transcription factor d: enrichment represented by a p-value for the in-house analysis or a coverage coefficient (cluster coverage divided by genome coverage) for the analysis with RSAT tool | |||||||||
van den Brink et al. BMC Genomics 2008 9:100 doi:10.1186/1471-2164-9-100 |
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