Table 1

Top 30 discovered motifs in the promoter regions as ranked by MCS scores

ID

Top Motifs

Genome wide statistics for the aligned region

Functional category enrichment*


N

k

C.R.

MCS

Most enriched functional category

Genes in functional category

Motif genes in Fun- Group

Enrichment Score


M1

CCCCnC

4734

1462

0.30

93.5

Nucleolus 1

128

75

11.9

M2

CACGTG

623

315

0.50

66.4

Ribosome 2

88

47

24.3

M3

CGTCAY

1970

468

0.23

41.6

Ribosome 2

88

53

5.0

M4

CGCGnC

2195

461

0.21

40.6

Nucleus 2

341

173

9.6

M5

CGCCnC

3007

525

0.17

37.2

-

-

-

-

M6

CCCCnG

2985

509

0.17

36.0

-

-

-

-

M7

CCnCCA

5444

767

0.14

35.4

Nucleus 2

341

178

7.9

M8

CTCCnC

4829

673

0.13

35.2

Peroxisome 2

32

24

5.4

M9

CnCCGMC

1857

357

0.19

33.8

Nucleolus 1

128

43

12.2

M10

CnCnCCC

4201

565

0.13

31.8

Nucleus 3

159

110

6.2

M11

CCAATnA

1105

212

0.19

30.6

-

-

-

-

M12

GCnnCGC

2624

385

0.14

29.3

Cytoskeleton 1

22

15

5.3

M13

ACGYSAC

797

173

0.21

27.9

Nucleus 2

341

150

6.7

M14

CCSGCC

1520

258

0.16

26.5

-

-

-

-

M15

CnGCnCC

3170

421

0.13

26.0

-

-

-

-

M16

CnTCnCC

5870

636

0.10

26.0

-

-

-

-

M17

ACCCCG

761

152

0.19

25.9

-

-

-

-

M18

CGGnCCG

369

93

0.25

25.2

-

-

-

-

M19

AAAAA

6137

668

0.10

24.5

Nucleolus 1

128

113

19.0

M20

CCnCnTC

5505

545

0.09

24.4

-

-

-

-

M21

AAAWTTY

853

169

0.19

23.7

Nucleolus 1

128

101

31.4

M22

TGCCCC

777

139

0.17

22.9

Nucleus 2

341

98

5.4

M23

GnGGCT

2449

321

0.13

21.5

-

-

-

-

M24

GCGCnC

1673

239

0.14

21.2

Nucleus 2

341

196

6.4

M25

TCCCnC

4141

432

0.10

20.8

-

-

-

-

M26

YGATAAG

393

85

0.21

20.2

Nucleolus 1

128

38

10.9

M27

CGACnnC

3725

399

0.10

19.9

-

-

-

-

M28

CCGCnGn

1874

245

0.13

19.7

-

-

-

-

M29

CCTCGGY

381

80

0.20

18.9

Peroxisome 2

32

22

13.5

M30

AnnCCAC

3708

373

0.10

18.6

-

-

-

-


Each motif shown here is the representative motif (i.e. the one with highest MCS score) from each cluster. N and k respectively represent the number of total occurrences in F.g. and the number of occurrences conserved in all four Fusarium genomes. C.R. is the conservation rate of the motif (= k/N) and MCS is the motif conservation score. * The promoter enrichment statistics is for the motif with the highest enrichment score (10th column) within each cluster shown in the 1st column. The names of the functional categories are derived from the GO annotation of F. g. The number associated with each category represents the cluster as identified by the k-means clustering on the expression data within each category. Enrichment score is in the unit of -log10(p-value).

Kumar et al. BMC Genomics 2010 11:208   doi:10.1186/1471-2164-11-208

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