Table 4. Canonical pathways affected by differentially expressed miRNA-mRNA pairs.

Ingenuity Canonical Pathways	P-value	Ratio (% of genes in pathway)	Dysregulated target gene	Dysregulated miRNA
Regulation of theEpithelial-to-Mesenchymal Transition Pathway	2.5 x 10–3	12/182 (6.6%)	CDH1, FGF2, FGF5, FGFRL1, ID2, LEF1, PARD6B, PDGFRB, TCF4, TGFB3, WNT7B, ZEB1	let-7i-5p, miR-29c-3p, miR-128, miR-129-5p, miR-148a-3p, miR-196b-5p, miR-205-5p, miR-299-3p, miR-342-5p, miR-381-3p, miR-654-5p, miR-2355-5p
IL-8 Signaling	7.39 x 10–3	11/183 (6.0%)	BCL2L1, CCND1, CDH1, GNG2, GNG4, HBEGF, IRAK2, ITGAV, PLCB2, RHOB, RHOG	let-7i-5p, miR-29c-3p, miR-146b-5p, miR-299-3p, miR-342-5p, miR-381-3p, miR-503-5p, miR-625-5p, miR-2355-5p
Clathrin-mediatedEndocytosis Signaling	7.68 x 10–3	11/184 (6.0%)	ARRB1, F2, FGF2, FGF5, GAK, HIP1, MDM2, PDGFB, SH3GL1, SH3GLB2, TFRC	let-7i-5p, miR-29c-3p, miR-133a, miR-148a-3p, miR-342-5p, miR-409-5p, miR-485-5p, miR-625-5p, miR-654-5p,
Wnt/β-catenin Signaling	1.02 x 10–2	10/166 (6.0%)	AXIN2, CCND1, CDH1, KREMEN1, LEF1, MDM2, TCF4, TGFB3, TGFBR3, WNT7B	let-7i-5p, miR-29c-3p, miR-128, miR-129-5p, miR-146b-3p, miR-148a-3p, miR-196b-5p, miR-205-5p, miR-299-3p, miR-376c-3p, miR-342-5p, miR-409-5p, miR-485-5p, miR-503-5p, miR-625-5p

The 480 differentially expressed genes targeted by miRNAs between SLKK and SLK cells were used as input for the Ingenuity pathway analysis (IPA). Here, we highlighted 4 of the top 10 enriched pathways that are relevant to KSHV pathogenesis. Columns identify the pathway name, its associated P-value, the ratio between dysregulated genes and genes in the pathway, which dysregulated target gene and miRNA are involved. Genes or miRNAs in bold and normal font were found up-regulated and down-regulated, respectively, by chronic KSHV infection.