Table 1

Known regulatory elements obtained when applying FastCompare to S. cerevisiae and S. bayanus

Name

Sequence

Rank

DATG

WATG

U/C

Motif

ChIP

Experiment

Best MIPS enrichment


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

Open Data