Close
Editor - Ruth Lovering
BHF funded PSICQUIC dataset
We are pleased to announce that Tony Sawford, at the EBI, has created a new PSICQUIC dataset that can be used in Cytoscape analysis. The EBI-GOA-nonIntAct dataset, which is updated every week, includes all of the GO Consortium protein interaction data and provides over 17,000 human protein interactions. These additional annotations increase the size of a microRNA processing network by 10%.
Gene annotation
We have expanded our annotation range to include the annotation of macromolecular complexes. Nancy received extensive training in complex annotation, from Birgit Meldal & Sandra Orchard (based at IntAct), and she has also been involved in discussions about the annotation of the Complex IDs with GO terms. We are pleased to announce the release of 13 macromolecular complexes on the IntAct Complex Portal (CP). These complexes have been created for a number of key model organisms including human, mouse and rat, and all are freely available. GO terms can be associated with Complex IDs, either using the IntAct CP or GOA editing tools. For example, Nancy has associated six GO terms with the telomerase catalytic core complex, using the GOA editing tool, and nine GO terms using the IntAct CP editing tool. The GOC and IntAct are working together to enable annotations created using both tools to be viewed in GO browsers.
Based on the EBI statistics, 18th July 2015, this project has associated over 34,000 GO terms to 4,600 gene products, 23,473 of which are to 2,542 human gene products. Along with 142 GO terms to 31 human miRNAs, and 139 GO terms to 19 non-human miRNAs. In addition, we have submitted 1,158 protein-protein interactions (PPIs) to IntAct, from the curation of 131 papers. All of our annotations are exported to public databases.
MicroRNA guidelines
Rachael has now completed the curation guidelines for consistent functional annotation of miRNAs and these are publicly available on the GO Consortium wiki. The guidelines, which were drawn up in consultation with the GO Consortium and experts in miRNA research, cover how a curator should translate into GO annotations the common experimental assays used to investigate miRNA function, including how to annotate experimentally verified targets of miRNAs as well as the physiological effects that silencing has on the cell or organism.
We also describe how to capture the context of miRNA function, e.g. in which cell or tissue types the miRNAs act - information that is essential for pathway analysis. Additionally, we provide guidance of which GO terms should be applied to the proteins of the miRNA biogenesis machinery, for example Dicer, in both animals and plants.
One of the key differences between microRNA annotations created by the UCL team and the GO Consortium and those created by several of the microRNA databases is in the treatment of transcription data. Many databases will use data that demonstrates that a microRNA is co-expressed with specific mRNAs as evidence that the microRNA regulates the level of these mRNAs. In contrast, GO curators will only annotate that a microRNA regulates specific mRNA levels based on experiments which knockdown or overexpress the microRNA.
Forthcoming meetings
At the end of August, Ruth and Rachael will be attending the GO Consortium meeting in Washington. In addition, they will both attend the first GO Consortium Symposium day, on September 1, which will be open to the research community and functional analysis tool providers.
Publications
Using Gene Ontology to describe the role of the neurexin-neuroligin-SHANK complex in human, mouse and rat and its relevance to autism. Patel S, Roncaglia P, Lovering RC. BMC Bioinformatics. 2015 Jun;6;16:186. PMID: 26047810
Contact goannotation@ucl.ac.uk to subscribe to this quarterly Newsletter