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Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks

(2009) Plant Physiology. 150(2). p.535-546
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Abstract
Analysis of gene expression data generated by high-throughput microarray transcript profiling experiments has demonstrated that genes with an overall similar expression pattern are often enriched for similar functions. This guilt-by-association principle can be applied to define modular gene programs, identify cis-regulatory elements, or predict gene functions for unknown genes based on their coexpression neighborhood. We evaluated the potential to use Gene Ontology (GO) enrichment of a gene's coexpression neighborhood as a tool to predict its function but found overall low sensitivity scores (13%-34%). This indicates that for many functional categories, coexpression alone performs poorly to infer known biological gene functions. However, integration of cis-regulatory elements shows that 46% of the gene coexpression neighborhoods are enriched for one or more motifs, providing a valuable complementary source to functionally annotate genes. Through the integration of coexpression data, GO annotations, and a set of known cis-regulatory elements combined with a novel set of evolutionarily conserved plant motifs, we could link many genes and motifs to specific biological functions. Application of our coexpression framework extended with cis-regulatory element analysis on transcriptome data from the cell cycle-related transcription factor OBP1 yielded several coexpressed modules associated with specific cis-regulatory elements. Moreover, our analysis strongly suggests a feed-forward regulatory interaction between OBP1 and the E2F pathway. The ATCOECIS resource (http:// bioinformatics.psb.ugent.be/ATCOECIS/) makes it possible to query coexpression data and GO and cis-regulatory element annotations and to submit user-defined gene sets for motif analysis, providing an access point to unravel the regulatory code underlying transcriptional control in Arabidopsis (Arabidopsis thaliana).
Keywords
GENOME-WIDE IDENTIFICATION, GENE-EXPRESSION MAP, DISCOVERY, THALIANA, DATABASE, MODULES, INFORMATION, CONSERVATION, PROMOTERS, SEQUENCES

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MLA
Vandepoele, Klaas, et al. “Unraveling Transcriptional Control in Arabidopsis Using Cis-Regulatory Elements and Coexpression Networks.” Plant Physiology, vol. 150, no. 2, 2009, pp. 535–46, doi:10.1104/pp.109.136028.
APA
Vandepoele, K., Quimbaya Gomez, M. A., Casneuf, T., De Veylder, L., & Van de Peer, Y. (2009). Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks. Plant Physiology, 150(2), 535–546. https://doi.org/10.1104/pp.109.136028
Chicago author-date
Vandepoele, Klaas, Mauricio Alberto Quimbaya Gomez, Tine Casneuf, Lieven De Veylder, and Yves Van de Peer. 2009. “Unraveling Transcriptional Control in Arabidopsis Using Cis-Regulatory Elements and Coexpression Networks.” Plant Physiology 150 (2): 535–46. https://doi.org/10.1104/pp.109.136028.
Chicago author-date (all authors)
Vandepoele, Klaas, Mauricio Alberto Quimbaya Gomez, Tine Casneuf, Lieven De Veylder, and Yves Van de Peer. 2009. “Unraveling Transcriptional Control in Arabidopsis Using Cis-Regulatory Elements and Coexpression Networks.” Plant Physiology 150 (2): 535–546. doi:10.1104/pp.109.136028.
Vancouver
1.
Vandepoele K, Quimbaya Gomez MA, Casneuf T, De Veylder L, Van de Peer Y. Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks. Plant Physiology. 2009;150(2):535–46.
IEEE
[1]
K. Vandepoele, M. A. Quimbaya Gomez, T. Casneuf, L. De Veylder, and Y. Van de Peer, “Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks,” Plant Physiology, vol. 150, no. 2, pp. 535–546, 2009.
@article{721930,
  abstract     = {{Analysis of gene expression data generated by high-throughput microarray transcript profiling experiments has demonstrated that genes with an overall similar expression pattern are often enriched for similar functions. This guilt-by-association principle can be applied to define modular gene programs, identify cis-regulatory elements, or predict gene functions for unknown genes based on their coexpression neighborhood. We evaluated the potential to use Gene Ontology (GO) enrichment of a gene's coexpression neighborhood as a tool to predict its function but found overall low sensitivity scores (13%-34%). This indicates that for many functional categories, coexpression alone performs poorly to infer known biological gene functions. However, integration of cis-regulatory elements shows that 46% of the gene coexpression neighborhoods are enriched for one or more motifs, providing a valuable complementary source to functionally annotate genes. Through the integration of coexpression data, GO annotations, and a set of known cis-regulatory elements combined with a novel set of evolutionarily conserved plant motifs, we could link many genes and motifs to specific biological functions. Application of our coexpression framework extended with cis-regulatory element analysis on transcriptome data from the cell cycle-related transcription factor OBP1 yielded several coexpressed modules associated with specific cis-regulatory elements. Moreover, our analysis strongly suggests a feed-forward regulatory interaction between OBP1 and the E2F pathway. The ATCOECIS resource (http:// bioinformatics.psb.ugent.be/ATCOECIS/) makes it possible to query coexpression data and GO and cis-regulatory element annotations and to submit user-defined gene sets for motif analysis, providing an access point to unravel the regulatory code underlying transcriptional control in Arabidopsis (Arabidopsis thaliana).}},
  author       = {{Vandepoele, Klaas and Quimbaya Gomez, Mauricio Alberto and Casneuf, Tine and De Veylder, Lieven and Van de Peer, Yves}},
  issn         = {{0032-0889}},
  journal      = {{Plant Physiology}},
  keywords     = {{GENOME-WIDE IDENTIFICATION,GENE-EXPRESSION MAP,DISCOVERY,THALIANA,DATABASE,MODULES,INFORMATION,CONSERVATION,PROMOTERS,SEQUENCES}},
  language     = {{eng}},
  number       = {{2}},
  pages        = {{535--546}},
  title        = {{Unraveling Transcriptional Control in Arabidopsis Using cis-Regulatory Elements and Coexpression Networks}},
  url          = {{http://dx.doi.org/10.1104/pp.109.136028}},
  volume       = {{150}},
  year         = {{2009}},
}

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