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Known regulatory elements obtained when applying FastCompare to S. cerevisiae and S. bayanus |
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| Name |
Sequence |
Rank |
DATG |
WATG |
U/C |
Motif |
ChIP |
Experiment |
Best MIPS enrichment |
|
|
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| Bas1 |
AAGAGTCA |
159 |
307 |
[0;500] |
1.24 |
BAS1 |
- |
2(1/1) |
Amino-acid metabolism (p < 10-6) |
| Cbf1 |
CACGTGA |
3 |
368 |
- |
2.70 |
CBF1 |
CBF1 |
6(3/3) |
Amino-acid metabolism (p < 10-6) |
| Ecm22/Upc6 |
TAAACGA |
59 |
362 |
[100;500] |
1.36 |
- |
- |
11(9/2) |
Lipid, fatty-acid and isoprenoid biosynthesis (p < 10-8) |
| Fkh1/2 |
TAAACAAA |
88 |
353 |
- |
1.73 |
FKH1 |
FKH2 |
2(1/1) |
- |
| Gcn4 |
TGACTCA |
160 |
323.5 |
[0;400] |
1.02 |
GCN4 |
GCN4 |
102(76/26) |
Amino acid biosynthesis (p < 10-29) |
| Gcr1 |
TGGAAGC |
260 |
663 |
[600:1000] |
1.24 |
GCR1 |
- |
4(4/0) |
- |
| Gis1 |
AAGGGAT |
207 |
402.5 |
[100;800] |
1.31 |
GIS1 |
- |
1(1/0) |
- |
| Hap4 |
CCAATCA |
114 |
540 |
[100:700] |
0.83 |
HAP4 |
HAP4 |
3(2/1) |
Respiration (p < 10-15) |
| Ino4 |
CATGTGA |
177 |
454 |
[100:1000] |
1.24 |
INO4 |
INO4 |
1(0/1) |
Lipid, fatty-acid and isoprenoid metabolism (p < 10-5) |
| Mbp1 |
ACGCGTC |
23 |
225 |
[0;600] |
3.25 |
MBP1 |
MBP1 |
29(18/11) |
DNA synthesis and replication (p < 10-11) |
| Met31 |
TGTGGCG |
302 |
424 |
[100;1000] |
1.35 |
MET31 |
MET31 |
4(4/0) |
- |
| Met4 |
CTGTGGC |
362 |
500 |
[100;800] |
1.08 |
MET4 |
MET4 |
1(1/0) |
Amino acid metabolism (p < 10-6) |
| Msn2/4 |
AAAGGGG |
49 |
332 |
[0;500] |
1.92 |
MSN2/4 |
- |
105(93/12) |
- |
| Gln3 |
GATAAGA |
143 |
434 |
[0;900] |
1.23 |
- |
- |
7(7/0) |
Nitrogen and sulfur metabolism (p < 10-6) |
| PAC |
GCGATGAG |
4 |
164.5 |
[0;400] |
6.77 |
PAC |
- |
141(28/113) |
rRNA transcription (p < 10-10) |
| Pdr3 |
CCGCGGA |
357 |
378 |
[0;500] |
2.34 |
PDR3 |
- |
18(15/3) |
- |
| Rap1 |
TGGGTGT |
110 |
498.5 |
[100;900] |
1.19 |
RAP1 |
- |
13(1/12) |
- |
| Reb1 |
CGGGTAA |
1 |
213 |
[0;1000] |
6.48 |
REB1 |
REB1 |
- |
- |
| Rox1 |
AACAATAG |
77 |
288.5 |
[0;500] |
2.05 |
- |
- |
1 (0/1)* |
- |
| Rpn4 |
TTTGCCACC |
20 |
175.5 |
[0;800] |
2.01 |
RPN4 |
- |
10(10/0) |
Cytoplasmic and nuclear degradation (p < 10-31) |
| RRPE |
AAAAATTTT |
2 |
188 |
[0;600] |
3.04 |
RRPE |
- |
167(31/136) |
rRNA transcription (p < 10-16) |
| Ste12 |
TGAAACA |
282 |
477 |
100;1000] |
1.15 |
STE12 |
STE12 |
5(3/2) |
fungal cell differentiation (p < 10-5) |
| Sum1/Ndt80 |
TGACACA |
51 |
385 |
[0;600] |
1.32 |
SUM1 |
SUM1 |
1(1/0) |
- |
| Swi4 |
CGCGAAA |
19 |
261 |
[0;600] |
3.25 |
SWI4 |
SWI4 |
39(22/17) |
- |
| TATA |
TATATAA |
18 |
291 |
[100;700] |
4.70 |
- |
- |
49(40/9) |
- |
| Ume6 |
TAGCCGCC |
6 |
457.5 |
- |
3.92 |
UME6 |
- |
- |
Meiosis (p < 10-7) |
| Xbp1 |
CCTCGAG |
219 |
348 |
[0;700] |
2.41 |
XBP1 |
- |
40(34/6) |
- |
|
For each known regulatory element, we show the best k-mer, its rank within the set of 398 highest-scoring k-mers, the median distance to ATG (for occurrences upstream of genes within the conserved set), the optimal window, the corrected ratio of upstream/coding bias, the best known motif (see Materials and methods), the best chromatin IP (ChIP) enrichment (see Materials and methods), the total (upregulated/downregulated) number of microarray conditions in which the k-mer was found (see Materials and methods), and the best MIPS enrichment. *This sequence was the most significantly over-represented 8-mer in the upstream regions of genes that were downregulated upon overexpression of the Rox1 gene (a known repressor of hypoxia-induced genes under aerobic conditions [95]), as part of a series of microarray experiments measuring S. cerevisiae transcriptional response to various stresses [96]. | |||||||||
Elemento and Tavazoie Genome Biology 2005 6:R18 doi:10.1186/gb-2005-6-2-r18 |
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