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UCL Institute of Cardiovascular Science

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February 2016

 

Editor - Ruth Lovering

Biocurators at UCL

We are very pleased to welcome Barbara Czub to our team. Barbara will spend 9 months covering Nancy Campbell's maternity leave and working with Rachael Huntley on microRNA (miRNA) annotations. Barbara has recently completed her PhD looking at why mutations in the ubiquitously expressed TOPORS gene cause only retinal degeneration, by identifying the retinal interacting partners of the TOPORS protein.  Jess moved on, to follow her more laboratory focused research career, and we wish her well in her new post.

Gene annotation

Based on the EBI statistics, 16th January 2016, the cardiovascular gene annotation team have associated 36,000 GO annotations with 5,000 proteins, 24,879 of which are to 2,760 human proteins. In addition, through the curation of 150 miRNA papers Rachael has annotated 55 human miRNAs, creating 500 GO annotations, as well as associating 245 GO terms with 44 non-human miRNAs. Ensembl Compara do not yet automatically transfer miRNA annotations across species, therefore Rachael has conservatively transferred annotations made to non-human species to the human equivalents, these annotations have the ISS (Inferred from Sequence and structural Similarity) evidence code.

These figures are an under-estimate of the true number of annotations that have been created, as the inclusion of complex annotation extension data, such as descriptions of the regulated gene targets of a single miRNA, are effectively additional annotation rows. Consequently, while Rachael has associated 745 GO annotations to 99 miRNAs, unrolling the annotation extensions associated with these identifies 1054 unique annotations.

The telomere project, undertaken by Nancy, Rachael and Jess, has resulted in a >200% increase in the number of telomere-relevant annotations in GO annotation data. To achieve this, new and existing GO terms were associated to 147 human proteins, including 49 that had no previous telomere-related annotations. As a result, there are currently 205 proteins with a total of 832 telomere-relevant annotations present in GO.

MSc student projects

Two Master's students, Alex Deng and Zara Umrao, will be joining us this year. Alex will be using GO to describe heart valve development, whereas Zara will be working with Rachael to curate the role of miRNAs in aortic aneurysm.

 

Forthcoming meetings

In April, Ruth will be attending Biocuration 2016 and the associated GO Consortium meeting, in Geneva

Meetings attended

At the end of last year Rachael presented the new miRNA curation guidelines at two RNA meetings, the 10th International Meeting on MicroRNAs, non-coding RNAs and Genome Editing in Cambridge, and the RNAcentral Consortium Meeting at EMBL-EBI. Then, in January, Ruth, Rachael, Jess and Barbara attended the UCL Cardiovascular Symposium, presenting 2 posters entitled "Using focused Gene Ontology curation to describe human telomere biology" and "Functional annotation of cardiovascular microRNAs with GO". The pdfs for these posters are available on the meeting page of our website.

Publications

Plasma urate concentration and risk of coronary heart disease: a Mendelian randomisation analysis. White J. et al. The Lancet. Online 15 Jan 2016. PMID:26781229.

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