July 2014

Editor - Paul Denny

The Parkinson's Gene Annotation team is developing a network of contacts with experts in the physiology, biochemistry and genetics of Parkinson's disease (PD). We have had some very stimulating discussions with colleagues at the Institute of Neurology, UCL and also at the MRC Centre for Neuropsychiatric Genetics and Genomics at Cardiff University. As a result, we have added the Wnt signaling pathway and endosomal transport to our annotation target list.

Gene Annotation

Our list of PD risk genes has grown, following talks with the IntAct team; the new genes are PM20D1, SETD1A and FAM47E and were originally identified in a meta-analysis of genome-wide association studies of PD. Over the next few months, we are focusing our annotation efforts on the regulation of neuron death, the cellular response to oxidative stress  and synaptic vesicle transport. Based on the EBI statistics, (7th June 2014), the team has associated 253 GO terms to 87 proteins, including 160 annotations to 51 human proteins.

Gene Ontology

Working with the GO editors to improve the Gene Ontology, we now have 24 new terms to better describe the biological roles of proteins associated with PD. We know that synaptic vesicle transport of dopamine is critical in PD, so we have contributed terms such as "synaptic vesicle recycling" and "synaptic vesicle recycling via endosome", which we have used to describe dopamine transport.

Community engagement

Over 30 biologists attended the seventh 2-day Bioinformatics and GO Annotation Workshop, led by Ruth, and the attendees submitted annotations for a variety of papers. This 2-day course provides hands-on training in the use of GO, as well as other bioinformatics resources, such as UniProt, Ensembl, IntAct and Cytoscape. Some of the papers chosen had a neurological theme; furthermore, we are particularly grateful that some people are continuing to contribute annotations. Helping the attendees was a valuable opportunity for Rebecca and I to refresh and clarify our thinking about annotation.

Call for contributions from the Parkinson's Community

The PD annotations will be substantially improved by expert contributions. Therefore, we would be grateful for any information, from scientists and clinicians, concerning the annotation of their "favourite" gene, perhaps suggesting, by email, what information is missing or inaccurate. GO annotations can be viewed in QuickGO, for example, the key PD gene, LRRK2, now has over 200 experimentally supported GO annotations, of which over 100 describe proteins bound by LRRK2.

Meetings Attended

Rebecca presented a poster at the UCL Neuroscience Symposium, London, 19th June entitled "Using the Gene Ontology to characterise key players in Parkinson's Disease".