The score of each path is computed on the basis of expression values of the genes catalyzing the enzymes involved in this path.
On the basis of the expression value, a gene is considered expressed or not in any given experiment.
For any gene i, it should arise from one of the J groups that are classified on the basis of two expression values with two treatments.
In addition, the tools that are available typically accept only gene lists as input and are not able to represent and analyze the continuous change, along the chromosome, of expression intensity assigned to overlapping regions of desired size, on the basis of the mean expression value calculated across all genes located in that region.
Next, on the basis of the mean expression value data, we constructed a Venn diagram for affiliation analysis (Figure 2A).
It is worth mentioning that we applied MFDA not on raw gene expression data here, but on log fold-changes relative to time point 0. The reason was that we wanted to group genes not on the basis of their absolute expression values, but on the basis of similar response to the stimulus.
Genes were selected on the basis of expression differences between the two microarray data sets and of absolute signal values (Table 1).
The R package annotationDbi [ 55] was used to obtain a full list of associations (along with higher-level terms) from annot8r annotations prior to analysis of GO term overrepresentation in gene sets selected on the basis of dn/ds or expression values.
The genes that appear in the prognostic list of a particular study were selected by ranking all the tested genes (for example, on the basis of the correlation of their expression values (measured over the training samples) with outcome.
On the basis of the expression stability values collected in this study, an optimal normalization factor for qRT-PCR data could be calculated using the three most stable genes (ACTB, hCypB, and Hprt1), and excluding the lowest-scoring GAPDH.
