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First, since we used an experimental system very similar to the one used in an experiment published elsewhere [ 9], we examined categories expected to have a number of genes differentially expressed based on this study.
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In this study, we found that none of the toxin cluster genes was identified to be differentially expressed based on the 2-fold difference in expression level and P value less than 0.0001 criteria.
Gene expression data indicates that in rice, about 48% of all predicted genes are expressed, based on the ratio of expressed transcriptional units (TU) to total TU (Knowledge-based Oryza Molecular biological Encyclopedia [ 36]).
Among these, 85 genes (62.04%) were expressed based on the EST data; while the microarray data indicated expression evidence for 60 genes (43.79%) (Additional file 7).
The economic parameters were expressed based on the system size.
The TAA and RAA were calculated and expressed based on the formula in the previous study [18].
The discharge ratios between "flow through orifice" and "flow over notch" were expressed based on the data.
The expression vector, pHASH102, produces any combination of promoter and open reading frame to be expressed based on the T-extended cloning method.
The effect of water backfill to saturate the coarse layers after the wetting front encounters the impeding fine layer is analytically expressed based on the active water content profiles.
A total 587 genes (∼2% of the total genes profiled) were differentially expressed based on the set analysis criteria.
Genes were randomly selected for real time qRT-PCR from the list of genes considered significantly differentially expressed based on the SAM results.
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