We use two measures of expression: breadth of expression (the number of tissues in which a gene was expressed) and maximum expression level among tissues (the highest value of expression of a gene among tissues).
Following [ 35], we used two measures of expression level: 1) breadth of expression, as the number of tissues in which a gene was expressed, and 2) maximum expression level across tissues.
As noted above, codon usage seems to be more related to the number of tissues in which a gene is expressed than to the maximum expression level in the different tissues.
The normalized data were then filtered by expression to exclude all probes that were expressed below 20% of the maximum expression level in at least one of the samples at each time point.
A tendency of maximum expression level at the middle of seed development was observed.
Another semaphorin protein, Sema2A, was documented to decrease by 2 4% of the maximum expression level over 10 μm (roughly 5 8% fractional change) in grasshopper's tissue sections46.
To compare expression across conditions, fluorescence divided by OD600 was normalized to the maximum expression level across all conditions following 12 h of induction with 5 ng ml−1 aTc.
Expression profiles are normalized by the maximum expression level of a given transcript across stages and hierarchically clustered using Cluster 3.0 and visualized as a heatmap using Java Treeview.
Expression profiles normalized by their maximum expression level across stages for these highly conserved completely novel transcripts were hierarchically clustered using Cluster 3.068 and visualized as a heatmap using Java Treeview69.
Assuming that the exogenously applied Sema3A worked to block the lower or higher end of the endogenous Sema3A gradient with different concentrations, this experiment possibly suggests a difference of endogenous Sema3A expression in the range of 0 1 μg/ml along the radial cortical axis, which is roughly equivalent to a change of ~1% maximum expression level over 10 μm distance.
Dictyostelium myosin II heavy chain could also be expressed in an inducible manner, although the induction ratio was not as high as β-galactosidase and the maximum expression level was not as high as wild-type levels.
