The mRNA expression indexes of the three target genes were calculated as previously described [ 15].
Expression indices of the HRneg- and Tneg-specific markers as well as the combined set of HRneg/Tneg markers were computed for each patient as follows: ∑ i ∈ P x i − ∑ j ∈ N x j n where x is the DWD-transformed expression, n is the number of genes within the signature, and P and N are the set of markers with positive and negative correlations with increased hazard, respectively.
The relative amounts of the target genes were evaluated by the relative expression index of mRNA using the 2(−△△C(T)) Method [ 44]: F = 10 △CT,T/AT) − (△CT,R/AR), where T represents the target gene, R refers to β-Actin, and △CT is the difference in the threshold cycle value (CT).
The expression index of GALT3 mRNA was calculated by the following formula: index= β-actin densindex= β-actinCs/β-actin density of a sample)×(GALthedensity of a sample/GALT3 density of the PBMCs).
To calculate the expression index of probe sets we used the PM model.
Furthermore, the expression index of Pax2 was closely related to histological grade of the tumor.
The expression index of Pax2 in well differentiated tumors was 1.88 ± 1.68, much lower than that in tumors of moderate (3.07 ± 1.96, P < 0.05) or poor differentiation (5.45 ± 2.76, P < 0.01).
Users can not only view expression value of a single lncRNA or protein-coding gene across 19 human normal tissues, but also simultaneously view the expression index of both lncRNA and protein-coding genes to learn about whether they are co-expressed across the 19 tissues.
The higher the histological grade, the higher positive rate and expression index of Pax2, indicating a high proliferative activity of cancer cells with many malignant biological behaviors such as invasion to the muscle wall, extrauterine spread and metastasis.
Despite the accuracy of the classifier for random forest-based class assignment in a test set of DC samples, the mean expression index of transcripts was low.
