title: Assessment of pleiotropic transcriptome perturbations in Arabidopsis engineered for indirect insect defence.
abstract: BACKGROUND
  Molecular characterization is an essential step of risk/safety assessment of genetically modified (GM) crops. Holistic approaches for molecular characterization using omics platforms can be used to confirm the intended impact of the genetic engineering, but can also reveal the unintended changes at the omics level as a first assessment of potential risks. The potential of omics platforms for risk assessment of GM crops has rarely been used for this purpose because of the lack of a consensus reference and statistical methods to judge the significance or importance of the pleiotropic changes in GM plants. Here we propose a meta data analysis approach to the analysis of GM plants, by measuring the transcriptome distance to untransformed wild-types.
  
  
  RESULTS
  In the statistical analysis of the transcriptome distance between GM and wild-type plants, values are compared with naturally occurring transcriptome distances in non-GM counterparts obtained from a database. Using this approach we show that the pleiotropic effect of genes involved in indirect insect defence traits is substantially equivalent to the variation in gene expression occurring naturally in Arabidopsis.
  
  
  CONCLUSIONS
  Transcriptome distance is a useful screening method to obtain insight in the pleiotropic effects of genetic modification.
authors.forename: Benyamin
authors.initials: B
authors.lastname: Houshyani
authors.forename: Alexander R
authors.initials: AR
authors.lastname: van der Krol
authors.forename: Raoul J
authors.initials: RJ
authors.lastname: Bino
authors.affiliation: Wageningen University, Plant Sciences Group, Laboratory of Plant Physiology, P,O, Box 658, Wageningen 6700 AR, The Netherlands. harro.bouwmeester@wur.nl.
authors.forename: Harro J
authors.initials: HJ
authors.lastname: Bouwmeester
mesh_terms: D000818:Animals; D017360:Arabidopsis / Q000235:genetics* / Q000469:parasitology*; D030541:Databases, Genetic; D017343:Genes, Plant; D005818:Genetic Engineering; D058685:Genetic Pleiotropy; D005838:Genotype; D007313:Insecta / Q000502:physiology*; D015999:Multivariate Analysis; D030821:Plants, Genetically Modified; D025341:Principal Component Analysis; D014158:Transcription, Genetic; D059467:Transcriptome / Q000235:genetics*; D019076:Transgenes / Q000235:genetics