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.

Lionikas et al. BMC Genomics 2012 13:592   doi:10.1186/1471-2164-13-592

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