Microarrays in ecological research: a case study of a cDNA microarray for plant-herbivore interactions

BMC Ecology
Matthias HeldIan T Baldwin

Abstract

Microarray technology allows researchers to simultaneously monitor changes in the expression ratios (ERs) of hundreds of genes and has thereby revolutionized most of biology. Although this technique has the potential of elucidating early stages in an organism's phenotypic response to complex ecological interactions, to date, it has not been fully incorporated into ecological research. This is partially due to a lack of simple procedures of handling and analyzing the expression ratio (ER) data produced from microarrays. We describe an analysis of the sources of variation in ERs from 73 hybridized cDNA microarrays, each with 234 herbivory-elicited genes from the model ecological expression system, Nicotiana attenuata, using procedures that are commonly used in ecologic research. Each gene is represented by two independently labeled PCR products and each product was arrayed in quadruplicate. We present a robust method of normalizing and analyzing ERs based on arbitrary thresholds and statistical criteria, and characterize a "norm of reaction" of ERs for 6 genes (4 of known function, 2 of unknown) with different ERs as determined across all analyzed arrays to provide a biologically-informed alternative to the use of arbitrary expre...Continue Reading

References

Aug 30, 2000·Proceedings of the National Academy of Sciences of the United States of America·M L LeeJ Sklar
Oct 9, 2001·Bioinformatics·K Y Yeung, W L Ruzzo
Mar 21, 2002·Molecular Ecology·Greg Gibson
Nov 28, 2002·Nature Genetics·Andrew J HollowayDavid D L Bowtell
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Nov 28, 2002·Nature Genetics·Rodrigo F ChuaquiMichael R Emmert-Buck
Jun 26, 2003·Annals of Botany·Mark W ChaseAlex S Parokonny

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Citations

Aug 5, 2010·Current Opinion in Lipidology·Gunilla Olivecrona, Thomas Olivecrona
May 9, 2013·Current Opinion in Pediatrics·Iris ReyhanBeth S Gottlieb
Dec 4, 2008·Comparative Biochemistry and Physiology. Toxicology & Pharmacology : CBP·Mikki G BoswellRonald B Walter
Jul 17, 2013·International Journal of Molecular Medicine·Barbara UszczyńskaMarek Figlerowicz
Mar 18, 2011·Plant, Cell & Environment·Matthias ErbTed C J Turlings
Apr 28, 2009·The Plant Journal : for Cell and Molecular Biology·Matthias ErbJurriaan Ton
Sep 30, 2017·Chemical Reviews·Amir Reza JassbiMeredith C Schuman

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Methods Mentioned

BETA
array technology
PCA
PCR

Software Mentioned

SPSS
Canoco

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