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

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

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

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%)

ISSN: 1479-5876