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Table 3 Discovered cis-regulatory clusters for Arabidopsis

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. 6a 95 AATCGC, ATCGCC, CCGACG, CCGATT, CCTCTC, CGATTT, CGCCGA, CTCCGA, CTCTCC, GACTGT, GCCGAC, TCCGAT, TCGCCG, TCTCCG cysteine-type peptidase activity 8 4.60E-11  
Fig. 6b 50 ACACGT, ACGTGT, CACGTG, CGTGTC response to water deprivation 11 1.50E-11  
    response to abscisic acid stimulus 12 7.90E-11  
    PP2C SIG 8 9.80E-11  
    Protein phosphatase 2C 8 1.20E-10  
Fig. 6c 61 CATGCA nutrient reservoir activity 12 1.80E-18  
    Seed storage protein 7 6.50E-16  
Fig. 6d 66 GGCCCA cytosolic ribosome 64 1.90E-103  
    cytosolic part 61 3.10E-99  
    ribosomal protein 65 3.00E-121  
    structural constituent of ribosome 65 8.10E-104  
Fig. 6e 47 CAACGG cell cycle 11 7.60E-13  
    cell division 10 2.00E-12  
Fig. 6f 17 GCACGT plant-type cell wall organization 8 9.80E-14  
    Extensin-like region 6 7.00E-13  
    structural constituent of cell wall 6 4.40E-11  
  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.