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

Table 3 Analysis of differential expression

		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***

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

ISSN: 1471-2164