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The striking similarities of these phenotypes reinforce the conclusions that we have drawn from an entirely objective gene expression analysis and suggest that the method provides an effective tool with which to explore the function of gata3 and other regulatory genes.
The Ct values were calculated using the real-time quantitative PCR analysis program, and the ΔΔCt values are equal to Ct objective gene – Ct β-actin; the relative value of the objective gene was equal to 2-ΔΔCt value.
As can be seen, the maximum number of target-centric networks contained only one objective gene linked to the target gene.
For these 1394 GO terms, we investigated whether particular GO terms were enriched in an objective gene list using Fisher's exact test.
The PlantTribes 2.0 database [ 28] is an objective gene family classification that can be used to investigate gene family composition and phylogeny on a global scale.
Creating a statistical model of the effect of inhibiting the target gene on expression of genes from the objective gene network encompasses two main steps.
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If there are interactions among the objective genes, breeding strategy must be addressed by the incorporation of the epistasis [51], [52].
All the genes interacting with the objective genes were analysed as potential knockout targets (further, target genes).
In the first step, the target-centric gene network is reconstructed, describing the interaction of the target gene with the objective genes that are its immediate neighbours, and also all direct connections of such objective genes.
These models were used to assess the knockout effect of target genes on the expression of objective genes.
Prediction of changes in expression levels of each of the m T objective genes after a knockout of the target gene was carried out using regression models corresponding to the objective genes.
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targeted gene
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