Regulatory motifs identified from a maize developmental coexpression network

Downs, G. S., Liseron-Monfils, C., Lukens, L. N. (March 2014) Regulatory motifs identified from a maize developmental coexpression network. Genome, 57 (3). pp. 181-184. ISSN 0831-2796

URL: http://www.ncbi.nlm.nih.gov/pubmed/24884692
DOI: 10.1139/gen-2013-0177

Abstract

Transcriptional control is an important determinant of plant development, and distinct modules of coordinated genes characterize the maize developmental transcriptome. Upstream regulatory sequences are often the primary factors that control gene expression pattern and abundance. Here, we identify 244 regulatory motifs that are significantly enriched within 24 gene expression modules previously constructed from transcript abundances of 34 876 Zea mays (maize) gene models from embryogenesis to senescence. Within modules, we identify motifs that have not been characterized. In addition, we identify motifs similar to experimentally verified motifs, and the functions of these motifs overlap with predicted module functions. This work demonstrates the power of transcript-level coexpression modules to identify both variants of known regulatory motifs and novel motifs that control a species' developmental transcriptome.

Item Type: Paper
Subjects: organism description > plant > maize
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression
organism description > plant
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes
CSHL Authors:
Communities: CSHL labs > Ware lab
Depositing User: Matt Covey
Date: March 2014
Date Deposited: 09 Oct 2014 17:07
Last Modified: 09 Oct 2014 17:07
Related URLs:
URI: http://repository.cshl.edu/id/eprint/30842

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