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Table 4 Two differentially expressed genes (Calcr, top table, and Adh7, bottom table) that are NOT detected by XBSeq, showing the exonic, non-exonic, and predicted true signals (estimated by using Eq.3), from 3 biologial 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 Calcr   
  WT (3 replicates) MYC (3 replicates)   
  1 2 3 μ σ 1 2 3 μ σ FC 1 p 2
Exonic 22 4 20 15.3 9.9 68 68 64 66.7 2.3 3.3 0
Non-exonic 64 4 64 44.0 34.6 193 218 199 203.3 13.1   
Predicted
true signal
0 0 0 0 0 0 0 0 0 0 0 1
  Read counts of gene Adh7   
  WT (3 replicates) MYC (3 replicates)   
  1 2 3 μ σ 1 2 3 μ σ FC 1 p 2
Exonic 633 438 429 500.0 115.3 827 1149 708 894.7 228.2 1.5 0.01
Non-exonic 430 241 322 331.0 95 643 771 513 642.3 129.0   
Predicted
true signal
203 197 107 169.0 53.8 184 378 195 252.3 109.0 1.2 0.53
  1. 1) FC denotes the fold-change of MYC vs WT, and 2) is the p-value from edgeR-robust (for Exonic read only) and XBSeq (for predicted true signal). Calcr was detected by all other four methods and Adh7 was detected by three methods except DESeq (p-value = 0.06).
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