UCL Institute of Cardiovascular Science


April 2014

Editor - Paul Denny

The UCL Gene Annotation team has started a new project, in collaboration between University College London and the European Bioinformatics Institute (EBI), funded by Parkinson's UK.

The Project team consists of:

Paul Denny (Co-ordinator, Biocurator)
Paul has wide experience in genomics, genotyping, sequencing and mouse models of disease. He has also curated and annotated human genetic variation databases, and is undergoing intensive training with the Gene Ontology.

Rebecca Foulger (Biocurator)
Rebecca has extensive experience as both a Gene Ontology (GO) annotator and a GO editor, having worked on the GO project for over twelve years. She recently co-ordinated a working group to revise the signalling domain of GO, and also been involved in outreach activities; teaching external institutions how to get the most from the Gene Ontology.

Ruth Lovering (PI)
Ruth has been leading the Gene Annotation team at UCL for six years and has considerable GO annotation experience.

Gene Annotation

We are taking three main approaches to prioritize targets for annotation, based on biological processes that are known to be relevant to Parkinson's disease (PD), proteins that are encoded by genes known to be associated with the risk of developing PD, or the proteins with which those proteins interact. These priorities will evolve in consultation with our grant co-applicant, Prof. John Hardy (UCL) and our Advisory Board. Thirty genes have been chosen based on published linkage or association studies and can be reviewed here. A dozen biological processes, including mitophagy, synaptic transmission and the unfolded protein response have been selected for focused annotation efforts. The protein interactions of three key proteins - LRRK2, SNCA and MAPT - are being captured in the IntAct database as part of a project funded by the MJ Fox Foundation. We are capitalizing on these data by prioritizing the annotation of the same papers that were identified by IntAct; this saves us the time-consuming process of checking the species origin of the proteins.

Gene Ontology

We have also begun the process of improving the Gene Ontology by adding new terms that better describe gene products relevant to Parkinson's disease. We will be guided in this effort by our Advisory Board.

Call for contributions from the Parkinson's Community

We ask scientists and clinicians to review the annotation of their "favourite" gene and suggest what information is missing, incomplete or inaccurate. GO annotations can be viewed in QuickGO and we welcome suggestions for GO annotations or papers to be used for annotation, by email.

Upcoming events

UCL Bioinformatics and GO workshop, 1-2 May 2014

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