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Table 1 Known regulatory elements obtained when applying FastCompare to S. cerevisiae and S. bayanus

From: Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach

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) -
  1. 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].
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