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Rice

Table 1 Motifs predicted by MAMA using microarray data from iron-deficient and -sufficient rice roots

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

Motif name

Score

P-value*

Annotations

ACGTACGT

1.881

3.03E-34

FAM1 motif

AGCTAGCT

1.880

2.73E-51

DCEp1 motif

CTATATAT

1.872

<1.0E-300

TATA-box motif

CATGCATG

1.867

<1.0E-300

IDEF1BS motif

CTAGCAGA

1.865

8.45E-13

 

CGCCACGT

1.862

6.57E-23

OsIRO2BS motif

AGTCAACT

1.860

7.54E-19

 

TGATCAAC

1.854

1.20E-13

 

ACTACGTA

1.853

1.21E-09

 

GCATGCTG

1.850

2.80E-10

Motif containing IDEF1 binding sequence

CAAGAATC

1.848

1.63E-09

IDEF2BS motif

CGCCTATA

1.845

1.34E-09

BRE U -TATA motif 1

TAGCTGCA

1.845

2.10E-06

 

TGGCGACA

1.843

1.88E-17

 

GCGCGCTA

1.843

4.18E-12

 

TAGCAAGT

1.842

8.53E-14

 

ACTGTAGC

1.838

2.22E-07

 

GTAGTACG

1.837

1.08E-04

 

ATGGCCAT

1.837

1.43E-13

 

CCTGAAGA

1.837

4.04E-04

 

GAACGTGT

1.836

1.06E-07

 

CATCAGCA

1.835

8.28E-12

 

TCGACGTG

1.834

2.34E-04

 

ATTAAGCG

1.833

3.43E-06

 

CTGGCACT

1.833

3.33E-04

 

TACTAGTA

1.831

3.89E-05

 

GCATATGC

1.83

3.16E-05

 

GTGACGTC

1.829

2.36E-03

 

AATACTCT

1.828

1.18E-07

 
  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 3.
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