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. 2016 Aug 31;6:32249. doi: 10.1038/srep32249

Figure 5. Differential expression analysis.

Figure 5

(A) Frequencies of genes differentially expressed (DE) at different fold changes, with Cuffdiff DE q-values < 0.05, expression above 5 FPKM in at least one condition, and minimum 3 fold difference. Up-/down-regulation in a group with high proportion of highly expressed genes relative to a group with low proportion of highly expressed genes. (B,C) Number of DE genes enriched in groups with high or low proportion of highly expressed genes, as marked, plotted across increasing FPKM thresholds (B), and ratio of enriched DE genes numbers in groups with high to low proportion of highly expressed genes, plotted across increasing FPKM thresholds (C). Shown DE genes criteria: fold-change ≥3, CuffDiff q-value ≤ 0.05, and expression ≥ FPKM threshold in every cell type comprising a group. (D) Average length of not DE and DE transcripts is not significantly different. Not DE transcripts selected based on expression above 1 FPKM, with FPKM value within 1% of each other, and Cuffdiff DE q-value > 0.05. DE transcripts selected based on expression above 1 FPKM in at least one condition, fold change 2 or above, and Cuffdiff DE q-value < 0.05 (mean ± SEM shown; independent samples t-test, N.S. = not significant).