Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses

BMC Genomics

Table 2 Exon-specific DexSeq analysis of expression of Irak2 gene

DexSeq-exonID	Irak2 exon	Normalised Mean Count comparison				DexSeq Statistical Results
		LG/J mean	SM/J mean	log2fold (S/L) Calculated from normlalised mean counts	P value	Disp Before Sharing	Disp Fitted	dispersion	log2 fold (S/L) DexSeq calculated	padjust
E001	1	0.21	0	0	0.3632	NA	NA	NA	NA	NA
E002	1	1.26	1	0	0.6956	0	2.04	2.04	2.13	1
E003	1	7.24	9.28	0.35	0.5647	0.4	0.2	0.4	2.83	0
E004	2	13.77	11.67	−0.02	0.9647	0.09	0.2	0.2	2.54	0
E005	3	6.33	3.3	−0.57	0.3403	0.17	0.48	0.48	2	0.8
E006	4	0.82	2.22	1.24	0.0819	0.47	1.41	1.41	3.75	0.76
E007	4	10.59	0.49	−4.03	0.0001	0.17	0.31	0.31	−1.75	1
E008	4	45.28	3.16	−3.48	0.0067	0.09	0.13	0.13	−0.91	1
E009	5	51.11	8.5	−2.67	0.0002	0.05	0.11	0.11	−0.24	1
E010	5	27.25	3.97	−2.53	0.0198	0.16	0.19	0.19	−0.14	1
E011	6	18.98	1.62	−2.94	0.017	0.12	0.23	0.23	−0.51	1
E012	7	2.67	0.24	−1.42	0.0424	0.3	1.59	1.59	−1.57	1
E013	8	17.32	2.33	−2.83	0.0019	0.18	0.21	0.21	−0.32	1
E014	9	11.27	0.62	−3.54	0.0041	0	0.41	0.41	−1.42	1
E015	10	39.58	2.95	−3.65	0.0009	0.06	0.14	0.14	−1.18	0.69
E016	11	31.23	4.41	−2.84	0.017	0.28	0.18	0.28	−0.41	1
E017	12	48.16	9.62	−2.4	0.001	0.03	0.12	0.12	0.03	1
E018	12	1.25	1.22	−1	0.2566	1.07	1.59	1.59	1.1	1
E019	13	0.8	0.49	0	0.4139	0.14	3.09	3.09	1.38	1
E020	13	3.13	0.24	−2.01	0.0004	0	1.07	1.07	−1.27	1
E021	13	39.8	4.41	−2.46	0.0021	0.16	0.13	0.16	0.06	1

The pattern of exons with the higher expression of normalised counts in LG/J samples (bold) corresponds to Irak2c splice variant. Irak2 foldchanges calculated from normalised mean counts show overexpression of exon-bins 7–17, 20 and 21 in the Irak2 gene model which standard DexSeq analysis failed to detect.
DexSeq-exonID – exon bins used by DexSeq; LG/J mean and SM/J mean – normalized count of reads per bin; Irak2 exons – Ensembl based exons, some exons were partitioned into several DexSeq bins; P-values – nominal p value of t-test between the LG/J and SM/J samples.

ISSN: 1471-2164