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Table 4 Overlap and consistency of DEGs detected by OneComp and SAM (FDR < 5%)

From: Statistically controlled identification of differentially expressed genes in one-to-one cell line comparisons of the CMAP database for drug repositioning

Dataset DEGs by SAM Sub-datasets DEGs by OneComp Overlap POG (%) Consistency (%)
GSE41326 1896 Sub 1 5084 1069 56.33 99.91
Sub 2 5217 1092 57.49 99.82
Sub 3 5440 1075 56.43 99.53
GSE7161 1280 Sub 1 4770 917 71.64 100.00
Sub 2 4595 932 72.81 100.00
Sub 3 4568 890 69.53 100.00
Sub 4 6973 909 70.94 99.89
GSE37820 633 Sub 1 3734 314 49.76 100.00
Sub 2 3657 327 51.82 100.00
Sub 3 3950 321 50.87 100.00
  1. Pair 1, 2, 3, 4 representing paired control and treated technical replicates 1, 2, 3, 4 within each dataset. Overlap denotes the common DEGs detected in each of the pairs by OneComp and the large dataset by SAM. Consistency denotes the percentage of overlapped DEGs that display the same deregulation direction (up- or down-deregulation) between OneComp and SAM (FDR < 5%). P denotes the significance of the consistency (binomial test). POG denotes the percentage of the DEGs identified by SAM (FDR < 5%) that are consistently detected by OneComp ((FDR < 5%)