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Table 6 Comparisons of the results obtained on simulated data

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

Induced variation of expression Gene Cuffdiff + TopHat (p-value <0.05) DESeq2 + Centroids (p-value <0.05) DESeq2 + RSEM (p-value <0.05) edgeR + Centroids (p-value <0.05) edgeR + RSEM (p-value <0.05) Same-expression Possibility Log2 Fold Change on centroids
Under FADS2    * ** ** 0.000 −1.01
Under PDE4DIP    * ** ** 0.529 −0.98
Under U2AF1    * ** ** 0.989 −0.82
Under WAC    * ** ** 0.000 −1.00
Under CLCA1    * **   0.000 −0.97
Under S100A8     ** ** 0.000 −1.04
Under BPG254F23.5    *    0.889 −0.88
Under EEF1A1    *    0.889 −0.95
Under LYZ    *    0.778 −0.91
Under SCGB1A1       0.000 −0.97
Over HLA-DQB1    * ** ** 0.778 0.99
Over IFI6    * ** ** 0.000 0.97
Over IGF1R    * ** ** 0.000 1.00
Over MUC5AC    * ** ** 0.000 1.01
Over POSTN    * ** ** 0.000 1.00
Over CD177    * **   0.222 0.99
Over HLA-DRA    * **   0.794 0.94
Over NSUN5P1    *   ** 0.889 0.90
Over UBBP4    *    0.778 0.98
Over MTRNR2L12       0.778 0.96
None DUX4L7    *    1 −0.02
None CH507-152C13.1    * *   0.995 −0.60
None AC016698.1    *    1 −0.06
None MRPL51P2      ** 1 −0.05
None CH507-152C13.4      ** 1 0.05
TP True Positives 0 0 17 13 11   
TN True Negatives 20,000 20,000 19,997 19,999 19,998   
FP False Positives 0 0 3 1 2   
FN False Negatives 20 20 3 7 9   
TP/(TP + FN) Sensitivity (recall) 0 % 0 % 85 % 65 % 55 %   
TN/(TN + FP) Specificity 100 % 100 % 99.9 % 100 % 99.9 %   
TP/(TP + FP) Precision 0 % 0 % 85 % 93 % 85 %   
  1. This table lists the results obtained on 10 over-expressed and 10 under-expressed genes. Five more genes are involved as false positives. Some workflows select the genes as significant DE events only by the p-value (*), while others compute also the correct FC (**). The first two workflows are not able to select significant p-values. Ten genes have a low uncertainty (same-expression possibility) and ten genes have a high uncertainty due to their multireads. The five false positive events have a same-expression possibility close to 1 and a non significant FC. Even in this case, there is an overall disagreement in the selection of DE genes. The last 7 rows of the table show some evaluation metrics about the results (Bold)
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