Functional Gene Annotation
The UCL based Functional Gene Annotation projects represent a collaboration between UCL, the Proteomic Services Group and Uniprot Content group at European Bioinformatics Institute (EBI) and Prof Manuel Mayr's group at King's College London. These projects are funded by the British Heart Foundation and Parkinson's UK.
The creation of protein-protein interaction networks is an essential step towards the unravelling of the complex molecular interactions in living organisms. Therefore, the UCL annotation team is contributing experimentally verified protein-protein interaction data. This data is submitted to the IMEx Consortium, via the IntAct database at EBI, following established IMEx consortium guidelines.
The Gene Ontology (GO) is the established standard for the functional annotation of gene products. GO vocabulary is a controlled vocabulary used to classify the following functional attributes of gene products: Biological Process (BP), Molecular Function (MF) and Cellular Component (CC). BP terms describe the biological processes a gene product is involved in, MF terms describe the molecular functions of a gene product and CC terms describe the subcellular or extracellular localisations of a gene product. Gene Ontology annotations are added directly to the Gene Ontology Annotation (Uniprot-GOA) database, at EBI.
GO terms are structured as directed acyclic graphs, where each term can have relationships to broader 'parent' terms or more specific 'child' terms. This hierarchical structure produces a representation of biology that allows for a greater amount of flexibility in data analysis than would be afforded by a format based on simple list of terms. See below the QuickGO image of the ancestral chart (Parent Ontology) for the term:'heart development'. LRRK2 provides an example of a comprehensively annotated protein.
By curating the scientific literature we will create an information-rich resource for the cardiovascular and Parkinson's-research communities, enabling researchers to rapidly evaluate and interpret existing data and generate hypotheses to guide future research. The impact of a focused annotation approach on data analysis is demonstrated in Alam-Faruque et al., 2011. Annotations contributed by the UCL annotation group to the GO Consortium, IntAct or IMEx datasets are listed as BHF-UCL (British Heart Foundation - University College London) or ParkinsonsUK-UCL (Parkinson's UK - University College London).
We welcome feedback and encourage researchers to review the annotation of their 'favourite' gene and suggest information that may be missing, inaccurate or incomplete in these annotations, or to suggest papers for annotation.
Comments and suggestions can be sent via
- email: firstname.lastname@example.org
Page last modified on 02 feb 15 12:12
The work of the Cardiovascular Gene Annotation group is supported by British Heart Foundation grant RG/13/5/30112. The work of the Neurological Gene Annotation group is supported by Parkinson's UK grant G-1307.