3.2  miRNA target prediction and integration of mRNA and miRNA expression profiles
To our knowledge, the resources available for the target prediction for EBV-encoded miRNAs to human 3′-UTR are limited; many of the public target prediction databases do not have the miRBase (release 19) for human miRNAs. Thus, we ran our in-house miRNA target prediction using scripts from Targetscan [36], PITA [37], and miRanda [38]. We ran the three prediction algorithms using the 149 miRNAs and UTR of the 2812 mRNAs, which are expressed significantly, as input. This resulted in 7951 miRNA–mRNA target pairs, which were predicted from at least two out of three algorithms with high efficacy. We further integrated transcript expression data into the predicted miRNA–UTR pairs to validate target pairs. We set the cutoff at two-fold for defining up/down regulation and focused on the pairs which are inversely expressed in terms of transcript expression. A total of 6423 target pairs were found inversely expressed in at least one combination of the expression comparisons. Of the 6423 target pairs, 4898 were inversely expressed in at least one NPC model system (HK1, C666, X666) against NP460, and 533 pairs are inversely regulated in all three NPC model systems against NP460 (Supplement 3).