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November 2017

Editor - Ruth Lovering

10 year anniversary

Today marks the 10 year anniversary of the UCL Functional Gene Annotation team based at the Rayne Institute, UCL. In that time the team has created GO annotations based on the review of over 5,000 experimental papers, and submitted over 3,200 molecular interactions to the IntAct database. Based on the EBI statistics, 21st October 2017, the cardiovascular gene annotation team has associated 42,562 GO annotations with 6,169 gene products, 29,442 of which are to 3,515 human gene products. The Functional Gene Annotation team was originally set up as a project within the HUGO Gene Nomenclature Committee (HGNC) with funding from the Wellcome Trust. But funding from the BHF enabled the project to become established as a group in its own right and begin the task of providing descriptive annotations for gene products relevant to cardiovascular disease. Since then funding by Parkinson’s UK and then Alzheimer’s Research UK has led to our annotation of gene products relevant to neurological diseases.

MSc student project 

Our Master’s student, Vanessa Acquaah, completed her annotation project in August, and since then has continued to work with us on a short project. Vanessa MSc project described the role of microRNAs in early heart development and created a total of 315 annotations, following the review of 49 papers. We are pleased to announce that she was awarded a Distinction.

Gene annotation

Since the release of our last newsletter 3 months ago, Nancy has increased the number of curated annotations in the IntAct database by an impressive 666 molecular interactions (could there be a halloween influence here?). This was achieved by curating two papers; firstly, 498 molecular interactions were added to the AMPK-α1 and AMPK-β1 interactomes in pancreatic beta-cells by curating a paper entitled: “Interactome analysis of AMP-activated protein kinase (AMPK)-α1 and -β1 in INS-1 pancreatic beta-cells by affinity purification-mass spectrometry”. Secondly, 168 molecular interactions were added to the human HSPB2 cardiac interactome by curating a paper entitled: “Characterization of the Cardiac Overexpression of HSPB2 Reveals Mitochondrial and Myogenic Roles Supported by a Cardiac HspB2 Interactome”. Vanessa, meanwhile, has associated over 500 GO terms, with around 150 gene products (mostly microRNAs) with a focus on describing cardiovascular angiogenesis.

Meetings attended

In September Rachael presented a poster entitled ‘Functional annotation of cardiovascular microRNAs with GO’ at the British Atherosclerosis Society meeting in Cambridge. While in October, the UCL-BHF-cardiovascular team attended the GO Consortium meeting in Cambridge, UK, where they contributed to several discussions with good results. For example, the GO Consortium agreed to include high quality high-throughput experimental data in the GO database, albeit using HTP-specific evidence codes, which Tony Sawford (EBI) implemented in the web-based tool Protein2GO. Also, prompted by Ruth, the Consortium agreed that recommendations and guidelines concerning future work with external groups are needed, for which drafts are now being written. Ruth also presented again the developing transcription factor decision tree, and it was agreed that additional work was needed and that progress should be discussed in the next meeting. Ruth also attended the GREEKC meeting in Lisbon, which continues to make progress in developing guidelines for the construction of a high quality and interoperable Knowledge Commons that covers the area of Gene Regulation information.

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