Skip to main content

Advertisement

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.