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Please use this identifier to cite or link to this item: http://hdl.handle.net/1942/17083

Title: Problems inherent to a meta-analysis of proteomics data: A case study on the plants' response to Cd in different cultivation conditions.
Authors: DUPAE, Joke
NOBEN, Jean-Paul
Carpentier, S.
Cuypers, Ann
Issue Date: 2014
Citation: Journal of Proteomics, 108, p. 30-54
Abstract: This meta-analysis focuses on plant-proteome responses to cadmium (Cd) stress. Initially, some general topics related to a proteomics meta-analysis are discussed: (1) obstacles encountered during data analysis, (2) a consensus in proteomic research, (3) validation and good reporting practices for protein identification and (4) guidelines for statistical analysis of differentially abundant proteins. In a second part, the Cd responses in leaves and roots obtained from a proteomics meta-analysis are discussed in (1) a time comparison (short versus long term exposure), and (2) a culture comparison (hydroponics versus soil cultivation). Data of the meta-analysis confirmed the existence of an initial alarm phase upon Cd exposure. Whereas no metabolic equilibrium is established in hydroponically exposed plants, an equilibrium seems to be manifested in roots of plants grown in Cd-contaminated soil after long term exposure. In leaves, the carbohydrate metabolism is primarily affected independent of the exposure time and the cultivation method. In addition, a metabolic shift from CO2-fixation towards respiration is manifested, independent of the cultivation system. Finally, some ideas for the improvement of proteomics setups and for comparisons between studies are discussed. Biological significance This meta-analysis focuses on the plant responses to Cd stress in leaves and roots at the proteome level. This meta-analysis points out the encountered obstacles when performing a proteomics meta-analysis related to inherent technologies, but also related to experimental setups. Furthermore, the question is addressed whether an extrapolation of results obtained in hydroponic cultivation towards soil-grown plants is possible.
Notes: Corresponding author at: Hasselt University, Agoralaan — Gebouw D, 3590 Diepenbeek, Belgium. Tel.: +32 11268326; fax: +32 11268229. E-mail addresses: joke.dupae@uhasselt.be (J. Dupae), sacha.bohler@uhasselt.be (S. Bohler), jeanpaul.noben@uhasselt.be (J.-P. Noben),sebastien.carpentier@biw.kuleuven.be (S. Carpentier), jaco.vangronsveld@uhasselt.be (J. Vangronsveld), ann.cuypers@uhasselt.be(A. Cuypers).
URI: http://hdl.handle.net/1942/17083
DOI: 10.1016/j.jprot.2014.04.029
ISI #: 000340315400003
ISSN: 1874-3919
Category: A1
Type: Journal Contribution
Validation: ecoom, 2015
Appears in Collections: Research publications

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