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Table 3 Analysis of differential expression

From: A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species

   Published transcriptomes Reciprocally re-annotated transcriptomes
Gene qPCR Gene length (# nucl.) DESeq2 DESeq2 + length matrix RPKM + limma RPKM + voom + limma Gene length (# nucl.) DESeq2
  log2FC D. mel D. mau log2FC log2FC log2FC log2FC D. mel D. mau log2FC
lace −0.19 1791 903 1.40*** 0.38 0.41 0.15 902 902 0.03
CG3558 0.08 3147 1956 1.50*** 0.67 0.75 0.26* 3150 3135 0.16
dac −0.29 3243 1878 1.47*** 0.57 0.65 0.18 1887 1878 0.46
RAF2 1.0e-03 3351 1854 1.77*** 0.84 0.94 0.31 1959 1966 0.33
Cp110 −0.18 1998 1218 2.31*** 1.38* 1.4** 0.55** 2000 1998 0.11
CBP −0.21 1653 894 1.42*** 0.35 0.54 0.14 1656 1653 −0.24
CG6766 −0.41 1575 852 1.81*** 0.79 0.88 0.25* 855 855 0.31
piwi −2.60** 2529 2526 −2.48*** −2.54*** −1.99** −1.08** 2532 2529 −2.48***
alrm −2.37*** 1413 1413 −6.54*** −6.67*** −4.93*** −2.68*** 1416 1416 −6.49***
Nplp1 1.04 1461 1461 3.85*** 3.63*** 3.06*** 1.50*** 1464 1464 3.80***
  1. Expression comparison is for D. mauritiana vs. D. melanogaster, thus a positive log2-fold change (log2FC) indicates higher expression in D. melanogaster and vice versa. *p < 0.05; **p < 0.005; ***p < 0.0005