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Rice

Table 2 Motifs predicted from a region 50 bp upstream to 150 bp downstream of TSS

From: Development of a novel prediction method of cis-elements to hypothesize collaborative functions of cis-element pairs in iron-deficient rice

Motif name

Sscore

P-value*

Annotations

CTATATAT

2.08

1.03E-69

TATA-box motif

AGCTAGCT

2.05

1.71E-86

DCEp1 motif

TATAAGTA

2.00

3.56E-05

 

CTTAATTA

1.99

3.68E-25

 

TGATCATG

1.99

2.57E-12

 

GCCTATAA

1.97

9.44E-08

BRE U -TATA motif 2

TATACACA

1.96

3.47E-15

 

TATAAAAG

1.95

1.19E-05

 

TAACTAGT

1.95

4.19E-10

 

GTCCTGTA

1.95

2.09E-08

 

CAACTATA

1.95

2.56E-07

 

CACTTAGT

1.94

6.14E-06

 

ACTGAAGT

1.93

6.06E-05

 

CATCAAGC

1.93

2.22E-08

 

GTACTACG

1.93

1.74E-07

 

ACATACCA

1.93

7.81E-09

 

AGTTGCAG

1.93

1.93E-11

 

GTACGTTC

1.93

7.25E-10

 

GCTATAGC

1.92

3.32E-08

 

CTAAGCTA

1.92

2.17E-09

 
  1. * P-values were calculated using a binominal test. Using 500 bp of upstream sequence from the TSS, the number of motifs in regulated genes and the number of every 8-bp sequence in regulated genes were compared from the number of motifs in all genes and the number of every 8-bp sequence in all genes. This P-value was not used to predict cis-acting motifs. These numbers used to calculate P-values and annotations using PLACE and TRANSFAC are shown in Additional file 5.
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