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 % |