Problems inherent to a meta-analysis of proteomics data: a case study on the plants' response to Cd in different cultivation conditions
| Autor: | Jean-Paul Noben, Ann Cuypers, Sebastien Carpentier, Joke Dupae, Jaco Vangronsveld, Sacha Bohler |
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| Rok vydání: | 2013 |
| Předmět: |
Proteomics
business.industry Biophysics Biology Carbon Dioxide Hydroponics Biochemistry Plant Roots Metabolic equilibrium Biotechnology Plant Leaves Oxygen Consumption Biological significance Stress Physiological Meta-analysis Proteome Botany Protein identification Statistical analysis business Cadmium Plant Proteins |
| Zdroj: | Journal of proteomics. 108 |
| ISSN: | 1876-7737 |
| Popis: | 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 CO 2 -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. |
| Databáze: | OpenAIRE |
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