Table 7.
snoRNA disturbances for Alström versus lean males
| snoRNA | Chr | Box | Host gene | Host gene function | Fold change |
P-value | FDR |
|---|---|---|---|---|---|---|---|
| Downregulated | |||||||
| U38B (SNORD38B) | 1q34.1 | C/D | RPS8 | Component of 40S ribosomal subunit | −1.8 | 0.01 | 0.18 |
| HBII-289 (SNORD89) | 2q11.2 | C/D | RNF149 | E3 Ubiquitin-protein ligase, implicated in pancreatic cancer |
−1.6 | 0.01 | 0.20 |
| HBII-95 (SNORD11) | 2q33.1 | C/D |
NOP5
NOP58 |
18S rRNA processing, modulated by sumoylation; implicated in Kennedy disease and breast cancer |
−1.6 | 0.005 | 0.12 |
| U99 (SNORA57) | 11q12.3 | H/ACA | METTL12 | 18S rRNA processing, putative methyltransferase | −1.8 | 0.001 | 0.07 |
| ACA64 (SNORA78) | 16p13.3 | H/ACA | SNHG9 | 28S rRNA processing, affiliated with long noncoding RNA |
−1.7 | 0.006 | 0.13 |
| ENSG207098 (SNORA70BL4) |
21q22.11 | H/ACA | AP000281.2 | Unknown function, known antisense gene transcript, processed pseudogene |
−3.7 | 0.001 | 0.06 |
| ENSG207002 (ACA5, SNORA5) |
3q21.1 | H/ACA | MYLK | Kinase phosphorylates myosin light chain to facilitate contraction, disease impact cardiovascular function |
−2.3 | 0.003 | 0.10 |
| ENSG239041 (snoU13 family) |
2q31-q32 | RAPGEF4 | Associated with COPD, pancreatitis, regulation of insulin secretion |
−2.1 | 0.009 | 0.17 | |
| ENSG238934 (ACA64 family) |
1q23.3 | DEDD | Scaffolding protein involved in apoptosis; ubinquinated in nucleus; facilitates and directs caspase-3 activity |
−1.8 | 0.005 | 0.13 | |
| ENSG252122 (ACA62, SNORA76 family) |
16q23.1 | CFDP1 | Important for cranial-facial development | −1.7 | 0.006 | 0.14 | |
| ENSG251992 (scaRNA17, U91) |
18q21.1 | C/D | 1. ACAA2 or 2. MYO5B |
|
−1.6 | 0.009 | 0.17 |
| Upregulated | |||||||
| U13 (SNORD13) | 8p12 | C/D | TTI2 | Gene interacts with TELO2, regulates PIP2 hydrolysis, damage response |
2.1 | 0.01 | 0.18 |
| U36B (SNORD36B) | 9q34.2 | C/D |
RPL7A (alt. SURF3) |
60S ribosomal protein, thyroid hormone receptor uncoupling protein |
1.6 | 0.003 | 0.10 |
| snR39B (SNORD2) | 3q27.3 | C/D | EIF4A2 | Initiation factor for translation with helicase activity, necessary for small rRNA binding |
1.6 | 0.009 | 0.17 |
| U75 (SNORD75) | 1q25.1 | C/D |
GAS5 (ncRNA) |
28S rRNA processing, growth arrest related to splicing |
1.5 | 0.002 | 0.07 |
| U23 (SNORA75) | 2q37.1 | H/ACA | NCL | Acid phosphoprotein in nucleolus, controls rRNA transcription by pol I, targets 18S rRNA |
2.5 | 0.005 | 0.12 |
| ACA45 (scaRNA15) | 15q25.2 | H/ACA | U2 snoRNA | FSD2 complementarity | 1.8 | 0.003 | 0.10 |
| ENSG252787 (SNORD19B) |
3p21.1 | GNL3 | Multiple splice variants; depletion or overexpression of gene inhibits proliferation in CNS |
1.8 | 0.002 | 0.08 | |
| ENSG238947 (snoU13 family) |
17q25.3 | CCDC57-18 | Multiple splice variants; unknown gene function; co-localized with fatty acid synthase which is elevated in uterine leiomyoma |
1.6 | 0.008 | 0.16 | |
| ENSG238657 (snoU13 family) |
9q34.2 |
RALGDS/
CELP |
Cellular signaling through Ras | 1.6 | 6.44E-05 | 0.01 | |
| ENSG252349 (SNORA31 family) |
17p11.2 | ALDH3A2 | Fatty aldehyde oxidation; associated with Sjogren-Larsson syndrome |
1.5 | 1.30E-05 | 0.01 |
Notes: Data resources: snoRNA Orthological Gene Database (snoopy, http://snoopy.med.miyazaki-u.ac.jp/); Gene Cards (http://www.genecards.org/); OMIM (http://www.omim.org/).
Abbreviations: alt, alternate; Chr, chromosome; CNS, central nervous system; COPD, chronic obstructive pulmonary disease; PIP2, phosphatidylinositol 4,5-bisphosphate; rRNA, ribosomal RNA; SNORA, small nucleolar RNA (H/ACA Box); SNORD, small nucleolar RNA (C/D Box); snoRNA, small nucleolar RNAs; TELO2, telomere maintenance 2.