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Table 2 Discovered cis-regulatory clusters for Saccharomyces cerevisiae

From: A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks

d-clust d-count related 6-mers Functional Cluster Name f-count P-val  
Fig. 4a 182 AAAATT, AAATTT, AATTTT, ATGAGC, CGATGA, CTCATC, GAGATG, GATGAG, GCGATG, TGAAAA, TGAGAT, TGAGCT, AAGGGG, AGGGGC, AGGGGG nucleolus 120 2.90E-129  
    ribosome biogenesis 90 2.30E-108  
    ncRNA processing 111 1.70E-94  
    90S preribosome 45 4.50E-47  
    nuclear lumen 127 1.20E-97  
Fig. 4b 85 TACACC, CCGTAC, CCATAC, ATCCGT, ACCCAT, ACATCC cytosolic ribosome 82 9.70E-131  
    ribosome 79 2.90E-128  
    structural constituent of ribosome 82 6.40E-111  
    cytosolic small ribosomal subunit 36 1.30E-51  
Fig. 4c 36 AACGCG, ACGCGA, ACGCGT, CGCGAA, CGCGTC, CGCGTT, GACGCG, TCGCGT chromosome 16 6.00E-11  
    cell cycle 23 9.00E-13  
    mitotic sister chromatid cohesion 9 9.40E-12  
    DNA metabolic process 19 6.60E-11  
Fig. 4d 13 GATAAG amide catabolic process 6 6.20E-13  
    purine metabolism 5 3.40E-11  
Fig. 4e 30 AAGGGG, AGGGGC, AGGGGG, response to temperature stimulus 21 6.30E-25  
    response to abiotic stimulus 21 8.10E-21  
    vacuolar protein catabolic process 14 4.20E-16  
Fig. 4f 7 GCACCC, GGGTGC iron transport 5 3.10E-09  
    iron ion transport 5 2.60E-08  
    siderophore transport 4 8.70E-08  
  1. 'd-clust' is the identifier for the discovered clusters; 'd-count' is the number of genes in the discovered cluster; 'f-count' is the number of genes in the functional clusters, which was discovered by previous well-organized experiments; 'P-value' is measured by Fisher's exact test p-value, which measures the enrichment level of the functions within the discovered cis-regulatory cluster relative to the genome.