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

BMC Genomics

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

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

Identified Motif Sequence: The motif sequence identified by MEME analysis in the promoter region of differentially expressed genes from the Clark genotype.
# of Seqs with Motif: The number of differentially expressed genes whose promoter regions contain the identified motif.
Motif E-Value: E-value of the motif assigned by MEME.
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.
TRANSFAC Binding Site Sequence: The transcription factor binding site sequence. Mismatched bases are between the identified motif and the reported binding sites are underlined.
TRANSFAC Annotation: The type of transcription factor that binds to the identified TFBS according to TRANSFAC.

ISSN: 1471-2164