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Table 2 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.

From: New insights into the Saccharomyces cerevisiae fermentation switch: Dynamic transcriptional response to anaerobicity and glucose-excess

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
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
  1. a: presence of the transcription factor in one of the clusters; NC = transcription factor not significant changed over time
  2. b: amount of genes in the genome belonging to the specified transcription factor
  3. c: amount of genes in the respective clusters or group of clusters belonging to the specified transcription factor
  4. 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
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BMC Genomics

ISSN: 1471-2164

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