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Table 2 Differentially expressed genes and correlation between calculated log2-fold changes and length difference between orthologous genes. Results are shown for the four applied methods, the three studied annotation strategies and the two described pairwise species comparisons

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

Method Annotation Species # Common genes # Differentially expressed genes (% of common genes)a Spearman’s p valueb FDR 0.05 Spearman’s rhob
DESeq2 Published D. mau vs D. mel 11,503 2,438 (21.2) 6.52e-33 *** −0.36
D. mau vs D. sim 10,023 2,974(29.7) 2.15e-20 *** −0.33
Direct D. mau vs D. mel 13,401 2,665 (19.9) 3.35e-20 *** −0.33
D. mau vs D. sim 13,328 3,710 (27.8) 5.90e-58 *** −0.57
Reciprocal D. mau vs D. mel 13,331 2,501 (18.8) 5.12e-02 n.s. −0.23
D. mau vs D. sim 13,320 3,508 (26.3) 1.48e-01 n.s. −0.29
DESeq2 + length matrix Published D. mau vs D. mel 11,503 1,192 (10.4) 2.24e-05 *** −0.13
D. mau vs D. sim 10,023 1,545 (15.4) 3.20e-02 a −0.08
Direct D. mau vs D. mel 13,401 1,259 (9.4) 1.07e-02 a −0.09
D. mau vs D. sim 13,328 1,957 (14.7) 5.24e-04 ** −0.13
Reciprocal D. mau vs D. mel 13,331 1,215 (9.1) 7.03e-01 n.s. −4.6e-02
D. mau vs D. sim 13,320 1,910 (14.3) 7.34e-01 n.s. −0.07
RPKM + limma Published D. mau vs D. mel 11,503 1,904 (16.6) 4.42e-04 *** −0.11
D. mau vs D. sim 10,023 2,427 (24.2) 1.06e-03 ** −0.12
Direct D. mau vs D. mel 13,401 1,890 (14.1) 5.68e-03 a −0.10
D. mau vs D. sim 13,328 2,795 (21,0) 4.49e-04 *** −0.14
Reciprocal D. mau vs D. mel 13,331 1,830 (13.7) 5.92e-01 n.s. −6.4e-02
D. mau vs D. sim 13,320 2,738 (20.6) 2.83e-01 n.s. −0.22
RPKM + voom + limma Published D. mau vs D. mel 11,503 1,853(16.1) 9.39e-04 *** −0.10
D. mau vs D. sim 10,023 2,204(22.0) 4.63e-02 a −0.07
Direct D. mau vs D. mel 13,401 1,899(14.2) 1.01e-02 a −0.10
D. mau vs D. sim 13,328 2,607(19.6) 5.92e-03 a −0.11
Reciprocal D. mau vs D. mel 13,331 1,819(13.6) 5.79e-01 n.s. −0.07
D. mau vs D. sim 13,320 2,519(18.9) 4.06e-01 n.s. −0.17
  1. aFDR 0.05
  2. bSpearman’s rank correlation is measured between log2FC and length difference of genes showing more than 49 bp length difference
  3. Published annotation: D. mau vs. D.mel: 1,038 genes/D.mau vs. D.sim: 764 genes; Direct annotation: D.mau vs. D.mel: 716 genes/D.mau vs. D.sim: 658 genes; Reciprocal annotation: D.mau vs. D.mel: 71 genes/D.mau vs. D.sim: 26 genes
  4. *p < 0.05; **p < 0.005; ***p < 0.0005