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Comparative co-expression analysis in plant biology

Sara Movahedi (UGent) , Michiel Van Bel (UGent) , Ken Heyndrickx (UGent) and Klaas Vandepoele (UGent)
(2012) PLANT CELL AND ENVIRONMENT. 35(10). p.1787-1798
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
The analysis of gene expression data generated by high-throughput microarray transcript profiling experiments has shown that transcriptionally coordinated genes are often functionally related. Based on large-scale expression compendia grouping multiple experiments, this guilt-by-association principle has been applied to study modular gene programmes, identify cis-regulatory elements or predict functions for unknown genes in different model plants. Recently, several studies have demonstrated how, through the integration of gene homology and expression information, correlated gene expression patterns can be compared between species. The incorporation of detailed functional annotations as well as experimental data describing proteinprotein interactions, phenotypes or tissue specific expression, provides an invaluable source of information to identify conserved gene modules and translate biological knowledge from model organisms to crops. In this review, we describe the different steps required to systematically compare expression data across species. Apart from the technical challenges to compute and display expression networks from multiple species, some future applications of plant comparative transcriptomics are highlighted.
Keywords
orthology, GENE-EXPRESSION ATLAS, ARABIDOPSIS-THALIANA, MICROARRAY ANALYSIS, TRANSCRIPTOME ATLAS, CORRELATION NETWORK, COMPARATIVE GENOMICS, expression analysis, comparative genomics, bioinformatics, RICE, DATABASE, MODULES, TOOLS

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Citation

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Chicago
Movahedi, Sara, Michiel Van Bel, Ken Heyndrickx, and Klaas Vandepoele. 2012. “Comparative Co-expression Analysis in Plant Biology.” Plant Cell and Environment 35 (10): 1787–1798.
APA
Movahedi, S., Van Bel, M., Heyndrickx, K., & Vandepoele, K. (2012). Comparative co-expression analysis in plant biology. PLANT CELL AND ENVIRONMENT, 35(10), 1787–1798.
Vancouver
1.
Movahedi S, Van Bel M, Heyndrickx K, Vandepoele K. Comparative co-expression analysis in plant biology. PLANT CELL AND ENVIRONMENT. 2012;35(10):1787–98.
MLA
Movahedi, Sara, Michiel Van Bel, Ken Heyndrickx, et al. “Comparative Co-expression Analysis in Plant Biology.” PLANT CELL AND ENVIRONMENT 35.10 (2012): 1787–1798. Print.
@article{3033907,
  abstract     = {The analysis of gene expression data generated by high-throughput microarray transcript profiling experiments has shown that transcriptionally coordinated genes are often functionally related. Based on large-scale expression compendia grouping multiple experiments, this guilt-by-association principle has been applied to study modular gene programmes, identify cis-regulatory elements or predict functions for unknown genes in different model plants. Recently, several studies have demonstrated how, through the integration of gene homology and expression information, correlated gene expression patterns can be compared between species. The incorporation of detailed functional annotations as well as experimental data describing proteinprotein interactions, phenotypes or tissue specific expression, provides an invaluable source of information to identify conserved gene modules and translate biological knowledge from model organisms to crops. In this review, we describe the different steps required to systematically compare expression data across species. Apart from the technical challenges to compute and display expression networks from multiple species, some future applications of plant comparative transcriptomics are highlighted.},
  author       = {Movahedi, Sara and Van Bel, Michiel and Heyndrickx, Ken and Vandepoele, Klaas},
  issn         = {0140-7791},
  journal      = {PLANT CELL AND ENVIRONMENT},
  language     = {eng},
  number       = {10},
  pages        = {1787--1798},
  title        = {Comparative co-expression analysis in plant biology},
  url          = {http://dx.doi.org/10.1111/j.1365-3040.2012.02517.x},
  volume       = {35},
  year         = {2012},
}

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