Table 3.
Association between Genes with and without Diagnostic GO Terms and Functional Features for Protein-Coding Genes Predicted to Have Different Types of Core Promoters
| Genes with/without Diagnostic GO Terms (Padja) |
||||
|---|---|---|---|---|
| Alternative Proxy | Inr Only and Inr/DPE | TATA/Inr | Motif 1/6 | DRE |
| Severe detrimental mutant phenotype | 70/9 (1.5 × 10−8) | 22/5 (8.2 × 10−3) | 13/3 (2.5 × 10−2) | 26/2 (1.3 × 10−3) |
| Expression during developmentb | ||||
| >80th percentile (E, P) | 88/84 (9.6 × 10−2) | 31/98 (1) | 18/78 (7.9 × 10−2) | 35/90 (6.1 × 10−1) |
| >95th percentile (E, P) | 87/78 (1.8 × 10−2) | 28/76 (1.7 × 10−1) | 18/60 (3.6 × 10−2) | 31/68 (2.1 × 10−2) |
| >80th percentile (E, P) and <40th percentile (L, AM, AF) | 87/61 (3.2 × 10−7) | 28/67 (2.5 × 10−2) | 17/58 (2.5 × 10−2) | 31/66 (4.9 × 10−2) |
| >95th percentile (E, P) and <40th percentile (L, AM, AF) | 86/59 (3.2 × 10−7) | 26/60 (3.2 × 10−2) | 17/49 (7.0 × 10−3) | 29/54 (1.2 × 10−2) |
Note.—Inr/DPE, initiator followed by downstream promoter element; TATA/Inr, TATA box followed by initiator; Motif 1/6, Motif 1 followed by Motif 6; DRE, DNA replication element binding factor.
aTwo-tailed Fisher's exact test; the Benjamini–Hochberg correction (Benjamini and Hochberg 1995) was applied to correct for multiple testing. For mutant phenotypes, the total number of genes for the two categories (severe vs. nonsevere) is 81/34 (Inr only and Inr/DPE), 29/18 (TATA/Inr), 43/20 (Motif 1/6), and 26/21 (DRE). For expression data, the total number of genes for the two categories is 91/94 (Inr only and Inr/DPE), 32/103 (TATA/Inr), 18/83 (Motif 1/6), and 35/100 (DRE).
bHigher than a given percentile in at least one timepoint during embryogenesis (E), pupa stage (P), or both and, if it is the case, lower than a given percentile in at least one timepoint in at least two stages among larva (L), adult male (AM), and adult female (AF).