Table 2

Discovered cis-regulatory clusters for Saccharomyces cerevisiae

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


'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.

Gao et al. BMC Genomics 2013 14(Suppl 1):S4   doi:10.1186/1471-2164-14-S1-S4

Open Data