Differentially expressed genes between two samples were identified by tophat and cufflinks softwares (Trapnell et al. [2009]; Roberts et al. [2011]), The P ≤ 0.05 and the absolute value of log2 Ratio ≥ 1 were chosen as the threshold to judge the significance of gene expression difference.
A list of detected microRNAs in each sample and the differentially expressed microRNAs between two samples were identified for each assay.
Differentially expressed genes between two samples were identified by fold change filtering.
Using filter settings for these threshold values, differences in the spot volumes between two samples were identified.
The different levels of methylation between studied samples were identified using the two-way hierarchical cluster analysis.
Differentially expressed genes between two samples were identified through Fold Change filtering as our previous research [ 27].
In this study, lncRNA expression profiling was performed on metastatic and primary NPC tumors, and the differentially expressed lncRNAs between these samples were identified.
Differentially-expressed miRNAs between the samples were identified according to the following two criteria: P ⩽ 0.001 and fold change of ⩾2.
To identify genes showing a significant change in expression during different developmental stages, the differentially expressed tags between two samples were identified by an algorithm developed by Audic et al. [ 29].
