Given that we used a log2-transformation, instead of the traditional X A ratio (described as X expression divided by autosome average expression), we used an index of log2 X expression) – log2(A expression) to describe patterns in relative X expression, or RXE.
Indexes of expression levels and genic parameters were log transformed prior to analysis.
It suggests that a quantitative estimate of the expression level by RCBS values performs better than other indices of expression measure.
The obtained images were then for a semi-quantitative analysis of the MAP2K3 expression by measuring the integrated absorbance (IA) using image analysis software Image-Pro Plus 6.0 (IPP6.0, Media Cybernetics, Silver Spring, MD, USA), and the average of the IA values of each sample was used as an index of the expression of MAP2K3 expression (Table 1) [ 33].
The reason for using CAI as an index of gene expression instead of taking advantage of the availability of gene expression data is that, in higher eukaryotes such as human, many genes are highly expressed only at specific time and in specific tissues.
An alternative index of gene expression is codon adaptation index, or CAI [31], which has been shown to correlate well with published gene expression in terms of mRNA level and protein abundance [22], [23], [32].
Call this the categorial index of the expression.
The use of CAI value [31] as an index of gene expression in human has been controversial [36], [37].
This AID/GAPDH ratio was then multiplied by 10,000 to provide a relative numerical index of AID expression that is adjusted for RNA content [ AID/GAPDH ×10,0000].
Many factors influence the selection of an optimal neighborhood size: the shape of the weighting window, the density of the network (i.e., average node degree), the choice of the index of differential expression (here, the logarithm of the fold change), and so on.
