Issue 11 - October 2010
Editor - Ruth Lovering
Over the summer Varsha has been co-ordinating a WNT signalling project http://gocwiki.geneontology .org/index.php/Wnt_signaling_Pathway. This annotation project is part of the Reference Genome project and has led to the annotation of 23 subfamilies of genes involved in WNT signalling, including WNT1-11, FZD1-10, AXIN1-2, CTNNB1 and LRP5, across 12 different species, by 12 different databases. WNT signalling plays an important role in heart development and Varsha provided a key role in choosing the annotations targets for this project and in discussions about the creation of new GO terms to describe this system (such as canonical Wnt receptor signaling pathway involved in heart development). Based on the EBI statistics, 21st September 2010, this project has associated 14,000 GO terms to almost 2,000 proteins, 11,000 of which are to 1340 human proteins. Furthermore, since September last year we have submitted 185 SourceForge requests, leading to the creation of 156 new GO terms.
The BHF-UCL team has encouraged last years Genetics of Human Disease MSc students to take part in an annotation competition, CACAO, being run by Jim Hu at Texas A&M University. The competition runs for eight weeks and encourages the students to submit annotations and challenge the accuracy of annotations made by other competitors. We obviously wish all the competitors luck (and accuracy) in this competition! In September we ran a 2-day GO annotation workshop at UCL. This was attended by 15 UCL scientists who learnt how to use some of the freely available biological databases, how to analyse high-throughput datasets and also contributed GO annotations directly to the GOA database. Following the success of this workshop we plan to run a second one in April 2011, please contact us if you are interested in attending
Changes to QuickGO
For those of you who use QuickGO you may have noticed an invitation on the front page to try to new beta version of QuickGO. Please do try using this site and let GOA team know if notice any problems, or like any features.
Ruth and Varsha attended the UCL partners Cardiometabolic Network meeting, London, in September. We were invited to give two 5 minute presentations, based on our posters, entitled ‘Bringing Gene Ontology to cardiovascular research’ and ‘Cross-species annotation of cardiovascular processes’. Also in September Ruth and Varsha attended the three-day GO Consortium (GOC) meeting, held in Bar Harbor, US, using webex and conference call facilities. Ruth presented the summary of the ‘Protein-binding’ working group. The focus of the meeting was the future direction of GO.
Ruth will be attending the Ontology Development and Engineering: Tutorial & Training Workshop at the EBI in October.
Fundamentals of gene ontology functional annotation Khodiyar VK, Dimmer EC, Huntley RP, Lovering RC, in Knowledge-based Bioinformatics: From analysis to interpretation, Book editors Gill Alterovitz and Marco Ramoni; 2010, Wiley: Boston, Massachusetts. p. 171-208.
Page last modified on 01 oct 10 11:35
The work of the Cardiovascular Gene Annotation group is supported by British Heart Foundation grant RG/13/5/30112