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Editor - Ruth Lovering
Biocurators at UCL
We are very pleased to welcome Dr. Rachael Huntley, who joins the Cardiovascular Gene Annotation team this month. Rachael has over 10 years experience as a Gene Ontology (GO) curator and in her previous position was Project Leader for the GOA project at the EMBL-European Bioinformatics Institute (EMBL-EBI). She will be responsible for the project providing GO annotation for miRNAs involved in cardiovascular-relevant processes. In addition, Dr Nancy Campbell returned to the team in September, after her maternity leave, and is now busy annotating telomerase and telomere-related proteins.
Gene annotation
Based on the EBI statistics, 25th October 2014, this project has associated over 31,500 GO terms to 4,300 proteins, 21,841 of which are to 2,436 human proteins. In addition, we have submitted 976 protein-protein interactions (PPIs) to IntAct, from the curation of 137 papers, which are now exported to public PPI databases.
Mila and Ruth worked together last month to complete the annotation of Bellemare et al. (2010), "Alternatively Spliced Products of the UGT1A Gene Interact with the Enzymatically Active Proteins to Inhibit Glucuronosyltransferase Activity In Vitro". The alternative use of various promoters, first, terminal and common exons at the UGT1A gene cluster leads to the production of 9 different functionally active UDP glucuronosyltransferases. However, this paper reported that use of an alternative terminal exon (exon 5b) leads to 9 additional alternatively spliced products (termed isoform 2s). These alternative isoforms are catalytically inactive and inhibit the activity of the isoform 1s. Bellemare et al. (2010) describe how 8 of the isoform 1s interact with 8 isoform 2s, thus they identified 64 PPIs. In order to capture these interactions the UniProtKB team were asked to create new isoform 2 specific identifiers. Once these identifiers were available Mila submitted the 64 PPIs to IntAct. However, these PPIs didn't reach the IntAct to GO export threshold, therefore, as these heterodimeric interactions impact on the activity of these enzymes, Ruth added these 64 PPIs to the GO database manually. In addition to the PPI annotations, the annotation of this paper led to the creation of a further 41 experimentally supported GO annotations, as well as 22 author statement GO annotations, leading to a substantial improvement in the annotations associated with this protein family. The 261 annotations associated with this paper can be viewed at QuickGO, the isoform information is available in the 'with' column.
Gene Ontology
During the past seven years we have requested the creation of nearly 1900 GO terms to enable detailed annotation of cardiovascular-relevant proteins. This represents 4.5% of the 40,000 GO terms currently available.
Meetings attended
In September Ruth attended the British Atherosclerosis Society meeting, presenting a poster entitled: The cardiovascular gene annotation initiative: current and future aims, and she was kept busy throughout the 1 ½ hour poster session. Ruth also attended the GO Consortium Barcelona meeting in October, where consistent approaches to annotation were discussed, along with new GO tools and facilities. Ruth also participated in a workshop to develop bioinformatics training for clinicians, at the Genome Analysis Centre, Norwich. This workshop set out a roadmap toward developing a bioinformatics training program designed for the needs of the health and medical researchers. With concept that if clinicians understand bioinformatics a plethora of genetic data becomes available to them.
We now have a twitter account @UCLgene, please follow us at: http://twitter.com/UCLgene
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