Skip to main content

Table 7 Rankings of the genes for the simulated data

From: A fuzzy method for RNA-Seq differential expression analysis in presence of multireads

Ranking Same-expression Possibility Cuffdiff + TopHat (p-value) DESeq2 + Centroids (p-value) DESeq2 + RSEM (p-value) edgeR + Centroids (p-value) edgeR + RSEM (p-value)
1 IGF1R false positive HLA-DRA PDE4DIP IGF1R PDE4DIP
2 POSTN CD177 MUC5AC WAC PDE4DIP POSTN
3 FADS2 CLCA1 FADS2 IGF1R WAC FADS2
4 MUC5AC EEF1A1 HLA-DQB1 U2AF1 FADS2 IGF1R
5 WAC false positive WAC HLA-DQB1 POSTN IFI6
6 CLCA1 FADS2 IGF1R FADS2 HLA-DQB1 WAC
7 IFI6 HLA-DQB1 POSTN MUC5AC U2AF1 U2AF1
8 S100A8 HLA-DRA PDE4DIP POSTN CLCA1 MUC5AC
9 SCGB1A1 IFI6 S100A8 HLA-DRA false positive S100A8
10 CD177 IGF1R CD177 EEF1A1 S100A8 NSUN5P1
11 PDE4DIP false positive EEF1A1 NSUN5P1 MUC5AC false positive
12 HLA-DQB1 LYZ CLCA1 false positive HLA-DRA false positive
13 LYZ MUC5AC IFI6 CD177 IFI6 HLA-DQB1
14 UBBP4 PDE4DIP UBBP4 CLCA1 CD177 CD177
15 MTRNR2L12 POSTN NSUN5P1 LYZ EEF1A1 HLA-DRA
16 false positive S100A8 LYZ false positive UBBP4 SCGB1A1
17 false positive U2AF1 MTRNR2L12 false positive SCGB1A1 CLCA1
18 HLA-DRA WAC SCGB1A1 IFI6 LYZ false positive
19 false positive false positive U2AF1 BPG254F23.5 NSUN5P1 LYZ
20 false positive false positive false positive UBBP4 MTRNR2L12 EEF1A1
  1. In order to highlight the true positives, the other genes are hidden by a “false positive” label