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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
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BMC Genomics

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