Differential regulation of transcripts in response to DENV1 infection.

Number of events in each category (Rows) predicted by Cuffdiff [40] (Top) and MISO [41] (Bottom) for Uninfected cells vs. DENV1-16007 infected cells (First column), Uninfected cells vs. DENV1-PDK13 infected cells (Second column). The number of up- and down-regulated events is also described for the gene and isoform categories. Superscript “a” indicates biological triplicates while superscript “b” indicates single measurement of the sample. Abbreviations used: differentially expressed genes (Genes exp), differentially expressed isoforms (Isoforms exp), differentially expressed transcriptional start site group (TSS group exp), differentially expressed coding sequence (CDS exp), differential coding output (CDS), differential promoter use (Promoters), differential splicing (Splicing), skipped exon (SE), mutually exclusive exons (MXE), alternative 3′ splice site (A3SS), alternative 5′ splice site (A5SS), alternative first exon (AFE), retained intron (RI) and tandem untranslated region (Tandem UTR).