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Table 7 Motifs in Promoter Regions of Differentially Expressed Genes Identified by MEME and Their Similarity to Transcription Factor Binding Sites in the TRANSFAC Database

From: Integrating microarray analysis and the soybean genome to understand the soybeans iron deficiency response

Identified Motif Sequence # Seqs withMotif Motif E-Value TRANS FAC Hit ID TRANS AC Binding Site Sequence TRANS FAC annotation
CATCCAACGGC 29 1.2E-1 M00227 TCCAACGGC Myb
CCCGCCACGCGCCAC 48 5.1E-26 M00187 GCCACGT GCC Helix Loop Helix
TGGCGGGA 50 5.8E-13 M00024 TGGCGC GA Elongation Factor 2
CCAAACCC 50 2.7E-5 No Hit   
CCACCACCACC 48 3.8E-16 No Hit   
ACACAACACAC 45 2.2E-10 No Hit   
AAAATAAAAATAAAA 9 2.27E-7 No Hit   
AATAAAAAAATAAAA 8 1.51E-7 No Hit   
AGCTAGCTAGC 6 1.47E-7 No Hit   
AGCGAGCGAGC 4 6.23E-8 No Hit   
AGCAAGCTAGC 3 2.47E-7 No Hit   
  1. Identified Motif Sequence: The motif sequence identified by MEME analysis in the promoter region of differentially expressed genes from the Clark genotype.
  2. # of Seqs with Motif: The number of differentially expressed genes whose promoter regions contain the identified motif.
  3. Motif E-Value: E-value of the motif assigned by MEME.
  4. TRANSFAC Hit ID: The TRANSFAC ID of the transcription factor binding site showing high homology to the identified motifs. Only three identified motifs showed homology to known transcription factor binding sites in the TRANSFAC database.
  5. TRANSFAC Binding Site Sequence: The transcription factor binding site sequence. Mismatched bases are between the identified motif and the reported binding sites are underlined.
  6. TRANSFAC Annotation: The type of transcription factor that binds to the identified TFBS according to TRANSFAC.