Table 2.
Relationship between Different Functional Features and Protein-Coding Genes Predicted to Have a Particular Type of Core Promoter
| Number of Genes Associated/Not Associated |
|||||
|---|---|---|---|---|---|
| Genomic Features | Inr Only and Inr/DPE | TATA/Inr | Motif 1/6 | DRE | Padja |
| Diagnostic GO terms (GO:0006355, GO:0007275) | 91/94 | 32/103 | 18/83 | 35/100 | 6.0 × 10−5 |
| Severe detrimental mutant phenotype | 81/34 | 29/18 | 26/21 | 43/20 | 1.6 × 10−2 |
| Expression profilesb | |||||
| >80th percentile (E, P) | 172/13 | 129/6 | 96/5 | 125/10 | 6.9 × 10−1 |
| >95th percentile (E, P) | 165/20 | 104/31 | 78/23 | 99/36 | 5.7 × 10−3 |
| >80th percentile (E, P) and <40th percentile (L, AM, AF) | 148/37 | 95/40 | 75/26 | 97/38 | 2.4 × 10−1 |
| >95th percentile (E, P) and <40th percentile (L, AM, AF) | 145/40 | 86/49 | 66/35 | 83/52 | 8.4 × 10−3 |
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.
aA randomization test of goodness-of-fit was performed for each genomic feature; P ≥ χ2 with 3 degrees of freedom (100,000 simulations). Subsequently, the Benjamini–Hochberg (Benjamini and Hochberg 1995) correction for multiple testing was applied.
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). Genes examined: with Inr only or Inr/DPE promoter types, 185; with TATA/Inr promoter type, 135; with Motif 1/6 promoter type, 101; and with DRE promoter type, 135.