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Table 3 Two differentially expressed genes (Nat1, top table, and Brca2, bottom table) that are ONLY detected by XBSeq, showing the exonic, non-exonic, and predicted true signals (estimated by using Eq.3), from 3 biological replicates for each WT and MYC mouse tissue.

From: Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads

  Read counts of gene Nat1   
  WT (3 replicates) MYC (3 replicates)   
  1 2 3 μ σ 1 2 3 μ σ FC 1 p 2
Exonic 63 47 77 62.3 15.0 91 110 120 107.0 14.7 1.3 0.15
Non-exonic 20 20 28 22.7 4.6 23 14 34 23.7 10.0   
Predicted
true signal
43 27 49 39.7 11.4 68 96 86 83.3 14.2 1.6 0.05
  Read counts of gene Brca2   
  WT (3 replicates) MYC (3 replicates)   
  1 2 3 μ σ 1 2 3 μt σ FC 1 p 2
Exonic 213 88 165 155.3 63.1 132 191 188 170.3 33.2 0.9 0.57
Non-exonic 216 77 142 145.0 69.5 90 108 101 99.7 9.1   
Predicted
true signal
0 11 23 11.3 11.5 42 83 87 70.7 24.9 4.3 0
  1. 1) FC denotes the fold-change of MYC vs WT, and 2) is the p-value from DESeq (for Exonic read only) and XBSeq (for predicted true signal).
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