Table 5.
Comparison of SCOREM with other methods in terms of detection of differential expression and functional enrichment
| Data Set | Standard (+FDR) | ANOVA | Custom CDF | SCOREM (+FDR) |
|---|---|---|---|---|
| Number of genes called differentially expressed | ||||
| GSE3678 | 1026 (1064) | 402a | 667 | 1405 (821) |
| GSE4051 | 2829 (2400) | 313a | 1678 | 3829 (1930) |
| GSE4799 | 2146 (323) | 832a | NAb | 4660 (298) |
| GSE9371 | 720 (102) | NA | 480 | 1550 (123) |
| BrCa | 73 (1137) | NA | NAb | 931 (592) |
| VSMC | 80 (92) | NA | 126 | 449 (53) |
| GonFat | 1753 (6005) | NA | 1966 | 4502 (3455) |
| IngFat | 777 (3925) | NA | 940 | 2989 (1782) |
| Average P-value of top 20 enriched GO categories | ||||
| GSE3678 | 4.5 × 10−10 (1.8 × 10−7) | 3.5 × 10−2a | 2.5 × 10−6 | 1.3 × 10−10 (5.1 × 10−9) |
| GSE4051 | 6.1 × 10−10 (5.1 × 10−8) | NA | 2.0 × 10−4 | 1.6 × 10−6 (4.9 × 10−8) |
| GSE4799 | 3.6 × 10−10 (5.3 × 10−9) | 1.2 × 10−2a | NAb | 2.0 × 10−13 (2.8 × 10−10) |
| GSE9371 | 6.1 × 10−7 (3.0 × 10−5) | NA | 8.6 × 10−6 | 1.8 × 10−9 (9.5 × 10−6) |
| BrCa | 3.6 × 10−4 (5.0 × 10−5) | NA | NAb | 6.3 × 10−5 (3.0 × 10−5) |
| VSMCc | NA (NA) | NA | 9.8 × 10−4 | 4.5 × 10−4 (NA) |
| GonFat | 3.2 × 10−15 (2.5 × 10−12) | NA | 1.2 × 10−9 | 8.3 × 10−13 (1.7 × 10−13) |
| IngFat | 1.6 × 10−8 (4.4 × 10−9) | NA | 7.9 × 10−6 | 3.5 × 10−8 (1.9 × 10−8) |
aNumber of differentially expressed genes or average P-values of top three or five GO categories as given in Ref. (4).
bNA indicates data sets with no raw data available, where the custom CDF approach could not be applied.
cP-values are for top 5 (Custom CDF) or top 10 (SCOREM) overrepresented GO categories; NA indicates fewer than five GO categories with any overrepresentation.