Table 1.
Significantly Upregulated miRNAs in Caenorhabditis elegans Dauer Larvae (FDR < 0.05)
| Rank | miRNA Gene | miRNA Family ID | Seed | Seed Conservationa | Seed Conservation Profilea | Log2 Fold Changes | Observed Function |
|---|---|---|---|---|---|---|---|
| 1 | miR-797 | miRNA family 50 | AUCACAG | mir-2/-43/-250 | +/+/+/− | 4.44 | Gonad migration (Brenner et al. 2010) |
| 2 | miR-4809 | miRNA family 37 | UAAGUUC | mir-1018/-4809/-4810 | −/−/−/− | 3.52 | — |
| 3 | miR-2210 | — | GGCAGAU | mir-72 | +/−/−/+ | 3.34 | — |
| 4 | miR-1824 | — | GGCAGUG | mir-34 | +/+/+/+ | 3.16 | DNA damage response (Kato et al. 2009) |
| 5 | miR-4807 | — | UGAGUUC | mir-983 | −/+/−/− | 2.76 | — |
| 6 | miR-248 | — | UACACGU | mir-248 | +/−/−/− | 2.75 | — |
| 7 | novel-miR-V_24974 | — | GGCUCAA | — | −/−/−/− | 2.19 | — |
| 8 | novel-miR-I_285 | — | GCGGGAC | — | −/−/−/− | 2.10 | — |
| 9 | miR-247 | miRNA family 26 | GACUAGA | mir-44/-61/-247/-279 | +/+/+/− | 1.94 | Gonad migration (Brenner et al. 2010) |
| 10 | miR-34 | miRNA family 31 | GGCAGUG | mir-34/-1824/-2227/-2239/-4933 | +/+/+/+ | 1.89 | DNA damage response (Kato et al. 2009) |
| 11 | miR-1 | miRNA family 4 | GGAAUGU | mir-1/-796 | +/+/+/+ | 1.85 | Synaptic transmission (Simon et al. 2008) |
| 12 | miR-1820 | — | UUUGAUU | mir-315 | +/+/+/+ | 1.59 | — |
| 13 | miR-791 | — | UUGGCAC | mir-791 | +/+/+/+ | 1.56 | — |
| 14 | miR-54 | miRNA family 40 | ACCCGUA | mir-51/-52/-53/-54/-55/-56/- 2233/-2237/-2271/-2274 | +/+/+/+ | 1.35 | Embryogenesis, pharynx attachment, developmental timing (Alvarez-Saavedra and Horvitz 2010; Brenner et al. 2010; Shaw et al. 2010) |
| 15 | miR-254 | — | GCAAAUC | mir-254 | +/−/−/− | 1.32 | — |
| 16 | miR-71 | miRNA family 30 | AUCACUA | mir-34/-71/-2953 | +/−/−/+ | 1.26 | Lifespan, AWC L/R neuron fate specification (de Lencastre et al. 2010; Boulias and Horvitz 2012; Hsieh et al. 2012) |
| 17 | miR-84 | miRNA family 1 | GAGGUAG | let-7, mir-48/-241/-795 | +/+/+/+ | 1.23 | Developmental timing, vulval cell fate specification (Reinhart et al. 2000; Abrahante et al. 2003; Lin et al. 2003; Abbott et al. 2005; Grosshans et al. 2005; Johnson et al. 2005) |
| 18 | miR-794 | miRNA family 1 | GAGGUAA | — | −/+/−/− | 1.14 | — |
Note.—Seed conservation column displays IDs of miRNAs that share a common seed within the phyla Nematoda. If the seed is not conserved in Nematoda, miRNA IDs from the subsequent phyla are displayed (in the order of Nematoda, Arthropoda, Lophotrochozoa, and Vertebrata). miRNA family ID is assigned if a miRNA is conserved at least once within C. elegans, P. pacificus, or S. ratti.
aNematoda/Arthropoda/Lophotrochozoa/Vertebrata.