Transcriptome-wide Gene Expression Analysis

We applied our original algorithm OncoFinder [12 ] for the functional annotation of the primary expression data and for the calculation of the PAS scores. The extracted raw microarray expression data were quantile normalized according to [44 (link)]. Our approach to the transcriptome-wide gene expression analysis applies processing of these results with the signalome knowledge base developed by SABiosciences (http://www.sabiosciences.com/pathwaycentral.php). The algorithm utilizes a scheme that takes into account the overall impact of each gene product in the signaling pathway but ignores its position in the pathway graph. The formula used to calculate the pathway activation strength (PAS) for a given sample and a given pathway p is as follows:
$PA{S}_p={\displaystyle \sum _{n}AR{R}_{np}}\cdot BTI{F}_n\cdot \lg (CN{R}_n)$
Here the case-to-normal ratio, CNR_n, is the ratio of expression levels for a gene n in the sample under investigation to the same average value for the control group of samples. The Boolean flag of BTIF (beyond tolerance interval flag) equals zero when the CNR value has passed simultaneously the two criteria that demark the significantly perturbed expression level from essentially normal. The first criterion is the expression level for the sample lies within the tolerance interval, where p > 0.05. The second criterion is the discrete value of ARR (activator/repressor role) equals to the following fixed values: −1, when the gene/protein n is a repressor of pathway excitation; 1, if the gene/protein n is an activator of pathway excitation; 0, when the gene/protein n can be both an activator and a repressor of the pathway; 0.5 and −0.5, respectively, if the gene/protein n is rather an activator or repressor of the signaling pathway p, respectively. The results for the 82 pathways were obtained for each sample (listed in the Supplementary dataset 2). The area-under-curve (AUC) values were calculated according to [28 ]. Statistical tests were done using the R software package.