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April 2018

Editor - Barbara Kramarz

ARUK-UCL Gene Ontology Curation Progress

The first goal of this project was to identify and annotate research articles describing the roles of a minimum of thirty proteins (priority list) implicated in processes involving the microtubule-associated protein tau (encoded by the MAPT gene). Based on the EBI statistics, 28th March 2018, 1428 ARUK-UCL GO annotations have been associated with 355 proteins since annotation of processes implicating tau began in July 2017. Among these, 964 GO annotations have been used to capture the roles of 182 human proteins, including the 33 proteins from the priority list. Together with the annotations we contributed previously through annotation of amyloid-beta receptors, the ARUK-funded projects have collectively resulted in a total of 3364  GO annotations to 513 proteins and/or protein complexes overall. The annotation work has additionally led to expansion of neurology-relevant branches of GO, resulting in 79 new ARUK-UCL GO terms (GOC statistics, 28th March 2018). We are currently seeking dementia-relevant datasets for (re-)analysis, which we could use to demonstrate that our contribution to the GO database will have resulted in more informative outcomes from high-throughput datasets analysed using GO.

ARUK-UCL: Focus on neuroinflammation

In April 2018 we are beginning the annotation of gene products involved in neuroinflammatory processes. We are going to continue to work even more closely with neurobiology researchers, whose expertise will be invaluable for managing the annotation priorities of this project. We will firstly sub-divide neuroinflammation into narrower, more specific neuroinflammatory aspects, and generate lists of proteins covering each aspect, which should be prioritised for annotation using GO.

30 Apr – 1 May 2018: Introduction to Bioinformatic Resources and GO workshop

This workshop, relevant to researchers working in any biological field, provides an overview of the available databases and resources as well as the GO curation process. Our group will answer your questions and help with your GO data analysis. The workshop is funded by the British Heart Foundation (BHF) and Alzheimer’s Research UK (ARUK). Please register using the Eventbrite link

Meetings attended

31 Jan – 2 Feb 2018: Paola attended the Conference on “Healthy Ageing: From Molecules to Organisms” in Hinxton, Cambridge, UK, where she was focused on identifying potential neuroinflammatory proteins for annotation.

12-15 February 2018: Ruth gave a talk about curation of gene regulation at the eCOST meeting Gene Regulation Ensemble Effort for the Knowledge Commons in Ljubliana, Slovenia.

1-2 March 2018: Barbara gave a talk about GO annotation of dementia-relevant proteins at the British Neuropathological Society (BNS) 119th Annual Meeting in London, UK.

19 March 2018: Barbara, Paola and Ruth hosted a project meeting with neurobiology experts Professors Paul Whiting and Nigel Hooper, Drs Rina Bandopadhyay and David Brough, and Elizabeth Wu. This meeting provided an overview of progress made on annotation of proteins involved in processes implicating amyloid-beta and tau, and it led to agreements about subsequent project priorities in the field of neuroinflammation.

20-21 March 2017: Ruth and Barbara attended the Alzheimer’s Research UK (ARUK) Conference in London, UK, where they presented a poster on GO curation and annotation of dementia-relevant proteins. Barbara’s poster led to discussions with several researchers interested in a variety of GO issues. In addition, we were pleased to see a number of posters including GO analyses, although several of the presenters noted the difficulty in deciding which enriched GO terms to list in their posters and papers. We have found that WebGestalt and g:Profiler are useful functional analysis tools to use, because they display the ontological relationships between the enriched GO terms.

Publications

Paul Denny, Marc Feuermann, David P. Hill, Ruth C. Lovering, Helene Plun-Favreau & Paola Roncaglia (2018) Exploring autophagy with Gene Ontology, Autophagy, DOI: 10.1080/15548627.2017.1415189

Videos

Many thanks to Kiran Musunuru for this brilliant Video Summary of Ruth’s latest paper on cardiac electrophysiology. The video elegantly summarises GO and its applications in scientific research.

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