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UCL Institute of Cardiovascular Science

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February 2014

 

Editor - Ruth Lovering

New Recruits

We are pleased to welcome Dr Paul Denny and Dr Mila Rodriguez-Lopez who joined us recently. Paul has a wide experience in genomics, genotyping, sequencing and mouse models of disease. He has also curated and annotated human genetic variation databases, however he will need some training in Gene Ontology (GO) annotation. Mila is covering Nancy's maternity leave and as she has previous experience in capturing protein-protein interactions she has not needed much training. Mila is focusing on annotating proteins identified as relevant to lipid traits, by GWAS.

Gene annotation

Based on the EBI statistics,  18th January 2014, this project has associated 29852 GO terms to 4,000 proteins, 20,506 of which are to 2,300 human proteins. In addition, we have submitted 445 protein-protein interactions (PPIs) to IntAct, following curation of 78 papers, which are now exported to public PPI databases. As mentioned in the November newsletter, all of these papers had been annotated using GO terms. We have now completed the re-annotation of papers describing telomere protection and maintenance, and have made substantial progress on those describing WNT signalling and lipid metabolism. 

We are pleased to announce that the UCL cardiovascular gene annotation initiative is now a member of the IMEx consortium and that our PPI annotations have the source BHF-UCL in the IntAct browser.

UCL Neurological Gene Annotation

The UCL Gene Ontology Annotation team is starting a new project, funded by Parkinson's UK, to apply functional annotation to human proteins that are relevant to Parkinson's disease (PD). We are using GO terms to annotate proteins that are either encoded by genes known to be associated with the risk of developing PD, or the proteins with which those proteins interact. Our key collaborator, Prof. John Hardy, also based at UCL, and our Advisory Board, will guide our priorities for annotation, but we also ask the wider research community for suggestions of papers and specific genes to annotate. We will be distributing a Neurological Gene Annotation Newsletter in the near future: please contact Paul Denny, the Parkinson's UK project co-ordinator, to sign up to this newsletter or to suggest papers or genes to annotate.

Community engagement

Our seventh 2-day Bioinformatics and GO Annotation Workshop (1-2 May 2014)  is now fully booked. This 2-day course provides hands-on training in the use of GO, as well as other bioinformatics resources, such as UniProt, Ensembl, Biomart, IntAct and Cytoscape. If you would be interested in having this course run in your department/group please contact Ruth Lovering.

 

Meetings attended

The team attended the November RA Fisher Centre for Computational Biology Meeting, in London, and Nancy presented a poster entitled: Gene Annotation at UCL. It was interesting to see that about half of the presentations and posters mentioned the use of Gene Ontology.

Upcoming meetings

In February the team will be attending two London meetings: the 2nd RA Fisher Centre Meeting, and the Crick Symposium - Rare Diseases. In addition, Ruth will be attending the March GO Consortium (GOC) meeting in College Station, Texas.

New Arrival

Congratulations to Nancy on the birth of her son Albrose, who arrived just in time for Christmas.


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