Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

Gene co-expression analysis has emerged in the past 5 years as a powerful tool for gene function prediction. In essence, co-expression analysis asks the question 'what are the genes that are co-expressed, that is, those that show similar expression profiles across many experiments, with my gene...

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Vydáno v:	Plant, cell and environment Ročník 32; číslo 12; s. 1633 - 1651
Hlavní autoři:	USADEL, BJÖRN, OBAYASHI, TAKESHI, MUTWIL, MAREK, GIORGI, FEDERICO M, BASSEL, GEORGE W, TANIMOTO, MIMI, CHOW, AMANDA, STEINHAUSER, DIRK, PERSSON, STAFFAN, PROVART, NICHOLAS J
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	Oxford, UK Oxford, UK : Blackwell Publishing Ltd 01.12.2009 Blackwell Publishing Ltd Blackwell
Témata:	Arabidopsis bioinformatics Biological and medical sciences Computational Biology correlation data collection Databases, Genetic Fundamental and applied biological sciences. Psychology gene expression Gene Expression Profiling Gene Expression Profiling - methods Gene Expression Profiling - statistics & numerical data genes Genes, Plant genetics methods Oligonucleotide Array Sequence Analysis Oligonucleotide Array Sequence Analysis - methods Oligonucleotide Array Sequence Analysis - statistics & numerical data plant biology Plants Plants - genetics prediction reverse genetics statistics & numerical data databases Correlation reverse genetics Arabidopsis Plant ecology Plant biology Arabidopsis thaliana Generation Cruciferae Dicotyledones Angiospermae Database Genetics Spermatophyta Experimental plant Bioinformatics
ISSN:	0140-7791, 1365-3040, 1365-3040
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Popis
Shrnutí:	Gene co-expression analysis has emerged in the past 5 years as a powerful tool for gene function prediction. In essence, co-expression analysis asks the question 'what are the genes that are co-expressed, that is, those that show similar expression profiles across many experiments, with my gene of interest?'. Genes that are highly co-expressed may be involved in the biological process or processes of the query gene. This review describes the tools that are available for performing such analyses, how each of these perform, and also discusses statistical issues including how normalization of gene expression data can influence co-expression results, calculation of co-expression scores and P values, and the influence of data sets used for co-expression analysis. Finally, examples from the literature will be presented, wherein co-expression has been used to corroborate and discover various aspects of plant biology.
Bibliografie:	http://dx.doi.org/10.1111/j.1365-3040.2009.02040.x Co‐first authors. ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 ObjectType-Review-3
ISSN:	0140-7791 1365-3040 1365-3040
DOI:	10.1111/j.1365-3040.2009.02040.x