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This initiative focused on the annotation of Parkinson's disease-relevant proteins and was funded by a 3-year Parkinson's UK grant (G-1307) from January 2014 to December 2016.
The Parkinson's UK-funded GO annotations have facilitated the detailed and high-quality annotation of over 800 Parkinson's disease-relevant genes, providing 4,500 GO annotations. There are many ways in with the impact of our curation on data analysis and annotation resources can be demonstrated. Annotations contributed by this project to the GO Consortium dataset are attributed to ParkinsonsUK-UCL.
For this initiative we created two priority gene lists.
- A high-priority set of 48 Parkinson's disease-relevant genes were selected based on genetic linkage or association studies (see table below).
Our longer Parkinson's-relevant priority list includes 329 gene products. These were chosen based on their interaction with high-priority gene products or because of their role in Parkinson's disease-related biological processes
- browse the Parkinson's-relevant protein list
GO annotations resulting from Parkinson's UK-funded projects
Priority Parkinson's processes
The following processes were prioritised, following discussions with experts in the field. These processes are considered to have important roles in Parkinson's disease.
- WNT signalling pathway
- Regulation of autophagy
- Mitophagy
- Endoplasmic reticulum unfolded protein response
- Synaptic vesicle transport
- Oxidative stress
- Regulation of neuron death
High-priority set of Parkinson's disease-relevant genes
Genes in this list were prioritised for comprehensive annotation using GO because variants in these genes have been implicated as having a role in Parkinson's disease, either in published linkage or association studies.
| HGNC symbol | HGNC name | PubMed Identifier | UniProt Identifier (human) |
| ACMSD | aminocarboxymuconate semialdehyde decarboxylase | 19943343 | Q8TDX5 |
| ATP13A2 | ATPase type 13A2 | 19943343 | Q9NQ11 |
| BST1 | bone marrow stromal cell antigen 1 | 9560156 | Q10588 |
| CCDC62 | coiled-coil domain containing 62 | 15349860 | Q6P9F0 |
| DDRGK1 | DDRGK domain containing 1 | 25064009 | Q96HY6 |
| DGKQ | diacylglycerol kinase, theta 110kDa | 22438815 | P52824 |
| EIF4G1 | eukaryotic translation initiation factor 4 gamma, 1 | 11462174 | Q04637 |
| FAM47E | family with sequence similarity 47, member E | 21738487 | Q6ZV65 |
| FBXO7 | F-box protein 7 | 19038853 | Q9Y3I1 |
| FGF20 | fibroblast growth factor 20 | 19943343 | Q9NP95 |
| GAK | cyclin G associated kinase | 22166458 | O14976 |
| GBA | glucosidase, beta, acid | 22166458 | P04062 |
| GCH1 | GTP cyclohydrolase 1 | 25064009 | P30793 |
| GIGYF2 | GRB10 interacting GYF protein 2 | 22166458 | Q6Y7W6 |
| GPNMB | glycoprotein (transmembrane) nmb | 21738488 | Q14956 |
| HIP1R | huntingtin interacting protein 1 related | 21738488 | O75146 |
| HTRA2 | HtrA serine peptidase 2 | 25422467 | O43464 |
| INPP5F | inositol polyphosphate-5-phosphatase F | 25064009 | Q9Y2H2 |
| LAMP3 | lysosomal-associated membrane protein 3 | 21738488 | Q9UQV4 |
| LRRK2 | leucine-rich repeat kinase 2 | 15541308 | Q5S007 |
| MAPT | microtubule-associated protein tau | 9500549 | P10636 |
| MCCC1 | methylcrotonoyl-CoA carboxylase 1 (alpha) | 12402251 | Q96RQ3 |
| MMP16 | matrix metallopeptidase 16 (membrane-inserted) | 12925570 | P51512 |
| NMD3 | NMD3 homolog (S. cerevisiae) | 12928496 | Q96D46 |
| NSF | N-ethylmaleimide-sensitive factor | 21812969 | P46459 |
| NUCKS1 | nuclear casein kinase and cyclin-dependent kinase substrate 1 | 19915575 | Q9H1E3 |
| PARK2 | parkin RBR E3 ubiquitin protein ligase | 21292315 | O60260 |
| PARK7 | parkinson protein 7 | 21292315 | Q99497 |
| PINK1 | PTEN induced putative kinase 1 | 21292315 | Q9BXM7 |
| RAB29 | RAB29, member RAS oncogene family | 21292315 | O14966 |
| RIT2 | Ras-like without CAAX 2 | 22451204 | Q99578 |
| SCARB2 | scavenger receptor class B, member 2 | 21738487 | Q14108 |
| SETD1A | SET domain containing 1A | 21738488 | O15047 |
| SIPA1L2 | signal-induced proliferation-associated 1 like 2 | 25064009 | Q9P2F8 |
| SLC41A1 | solute carrier family 41 (magnesium transporter), member 1 | 19915576 | Q8IVJ1 |
| SLC45A3 | solute carrier family 45, member 3 | 19915576 | Q96JT2 |
| SNCA | synuclein, alpha (non A4 component of amyloid precursor) | 21292315 | P37840 |
| STBD1 | starch binding domain 1 | 21738488 | O95210 |
| STK39 | serine threonine kinase 39 | 21738488 | Q9UEW8 |
| STX1B | syntaxin 1B | 21738488 | P61266 |
| SYNJ1 | synaptojanin 1 | 23804577 | O43426 |
| SYT4 | synaptotagmin IV | 22451204 | Q9H2B2 |
| SYT11 | synaptotagmin XI | 21292315 | Q9BT88 |
| TAF1 | TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa | 21292315 | P21675 |
| UNC13B | unc-13 homolog B (C. elegans) | 21812969 | O14795 |
| VPS13C | vacuolar protein sorting 13 homolog C (S. cerevisiae) | 25064009 | Q709C8 |
| VPS35 | vacuolar protein sorting 35 homolog (S. cerevisiae) | 21292315 | Q96QK1 |
| WNT3 | wingless-type MMTV integration site family, member 3 |
HUGO Gene Nomenclature Committee (HGNC) approved gene symbols and names are listed, the PubMed identifiers indicate the publication describing the association with Parkinson's disease, and the UniProt IDs link to the QuickGO Gene Ontology annotations for each protein. Genes identified in genome-wide association studies are those suggested by the authors to be the most likely candidates and genes known to contain causative variants are highlighted in bold font.
Image credit: By Emw (Own work) [CC BY-SA 3.0 (http://creativecommons.org/licenses/by-sa/3.0) or GFDL (http://www.gnu.org/copyleft/fdl.html)], via Wikimedia Commons