UCL Institute of Cardiovascular Science


Issue 19 - October 2012


Editor - Ruth Lovering

Gene annotation

Based on the EBI statistics, 1st September 2012, this project has associated almost 27,000 GO terms to 3,700 proteins, 18,500 of which are to 2,150 human proteins. Ruth has continued to annotate key genes involved in cardiac conduction processes, such as CACNA1D, CASQ2, CAV3 and KCNA5. In contrast, Varsha has focused on the phenomena of heart jogging, which has been described in zebrafish. This is process occurs early in heart development, but does not seem to occur in mammals. Several zebrafish genes have been identified as playing a role in heart jogging and Varsha has been annotating the mammalian orthologs of these genes. Thanks go to Doug Howe, at ZFIN, for his help with this annotation project.

This year we have had an MSc project student, Greg Rowe, creating annotations. The focus of his project was to capture the role of NOTCH signalling pathway genes in heart development. His review of 32 papers created 588 annotations to 60 proteins. The majority of the experimentally supported annotations were to mouse proteins, however this information has been transferred to the human ortholog whenever possible.

Gene Ontology

New GO terms describing cardiac conduction are continuing to be released; with many more still to come. This brings the total number of GO terms created through the focused annotation of cardiovascular-relevant genes to almost 1600. In September the GO Consortium decided that it would remove all cellular fractionation GO terms, such as membrane fraction, synaptosome. The BHF-UCL team reviewed 180 annotation using these GO terms, in some cases alternative GO terms were applied, but many annotations were deleted.  


Community annotation

UCL students and staff annotated 18 papers during our July GO curation day, allowing Varsha and Ruth to submit around 80 annotations from these papers to the GO Consortium. Further annotations were also submitted during the September workshop, where the PomBase community annotation tool was used for the first time to create human GO annotations. Our thanks go to all attendees for their contributions and to the PomBase team for their help and for modifying their tool for our use.

If you would like to improve the annotation or your favourite gene, please note that registration is now open for our sixth GO Annotation Workshop (18-19th April 2013). As always this workshop is freely available to all biological or biomedical PhD and Post-Doc research scientists. The workshop aims to boost attendees' understanding of bioinformatics resources and their use. Please register for the April workshop, or contact us if you are interested in attending a future workshop.

Website Updated

Varsha has been working with Sonja Van Praag, from Information Systems, to create a new look for our website, in keeping with the UCL web corporate identity. We hope our visitors find it easier to access the information they are looking for. Many thanks to Sonja for her help with this.

Meetings attended

In July Varsha attended the 12th London Heart Development Meeting at the Institute of Child Health and in September Ruth attended the Cambridge University Genetics Centenary Symposium. 

Upcoming meetings

Ruth will be remotely attending the October GO Consortium meeting, which is being held in Caltech, Pasadena.





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