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February 2017

Editor - Ruth Lovering

Gene annotation

Based on the EBI statistics, 14th January 2017, the cardiovascular gene annotation team has associated 40,900 GO annotations with 5,900 gene products, 28,000 of which are to 3,375 human gene products. GO annotations have been provided by biocurators at UCL for over 12 years now, contributing 36,000 annotations to human gene products. We are also pleased to announce that as part of our neurological annotation initiative we are now starting a 6-month ARUK funded annotation project. For this project Barbara will focus on using GO terms to capture the role of Alzheimer’s disease-relevant amyloid-beta binding proteins. Email us for more information about this project.

miR-29 Annotation Impact

Molecular interaction data

Using the new pipeline generated by Tony Sawford, it is now possible to use Cytoscape and BiNGO to overlay GO terms onto a microRNA:mRNA network (see figure on right). However, this requires a bit of identifier editing, therefore, we have created a new page with tips on how to use Cytoscape on our website. If you would like to contribute any other helpful suggestions to this page please email us.

Meetings attended

In November Ruth attended the GO Consortium meeting in Los Angeles, where she led three discussions on guidelines covering annotation of: transcription factors; 'integral to membrane' proteins; high-throughput experiments. This resulted in an agreement that proteins with transmembrane domains could be annotated to relevant 'integral to membrane' terms, when supported by experimental evidence, such as immunofluorescence. Also it was agreed that experimental evidence demonstrating that a protein was an RNA polymerase II transcription factor could be used to support the association of the GO term nuclear chromatin with the protein. Guidelines for annotation of high-througput data and transcription factors are continuing to be discussed.

Promoting alternative careers

Rachael is co-organising a meeting entitled "Professional Careers: Where can your PhD take you?” to be held at UCL on 7th November. The meeting will showcase careers for cardiovascular scientists who have completed their Ph.D. or post-doctoral studies and who do not wish to follow a traditional academic route. Please visit the registration page for more details.

Publications

The Gene Ontology Consortium. (2017) Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Res. 4;45(D1):D331-D338. PMID:27899567

Ferrari R, Lovering RC, Hardy J, Lewis P, Manzoni C. (2017) Weighted protein interaction network analysis of Frontotemporal Dementia. J Proteome Res. Jan 12. [Epub ahead of print]. PMID:28004582.

Sunderland N, Skroblin P, Barwari T, Huntley RP, Lu R, Joshi A, Lovering RC, Mayr M. (2017) MicroRNA Biomarkers and Platelet Reactivity - the "Clot" Thickens Circ Res. 120(2):418-435. PMID:28104774.

Evans IM, Kennedy SA, Paliashvili K, Santra T, Yamaji M, Lovering RC, Britton G, Frankel P, Kolch W, Zachary IC. (2016) VEGF promotes assembly of the p130Cas interactome to drive endothelial chemotactic signalling and angiogenesis. Mol Cell Proteomics. Dec 22. [Epub ahead of print]. PMID:28007913.

Lovering RC. (2017) How Does the Scientific Community Contribute to Gene Ontology? In The Gene Ontology Handbook. C. Dessimoz, N. Škunca (editors). Springer: New York City, USA. Methods Mol Biol. 1446:85-93. PMID:27812937.

Huntley RP, Lovering RC. (2017) Annotation Extensions. In The Gene Ontology Handbook. C. Dessimoz, N. Škunca (editors). Springer: New York City, USA. Methods Mol Biol. 1446:233-243. PMID:27812947.

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