We are using the GOA-Uniprot curation tool to associate Gene Ontology (GO) terms with cardiovascular-relevant proteins, this data is then incorporated into the GOA-Uniprot database and the GO Consortium database. We are also capturing protein-protein interaction data using the IntAct editing tool and these annotations are directly incorporated into the IntAct database, and then included into the IMEx Consortium database. All of our annotations are then propagated to popular freely available online knowledgebases, such as UniProt, Ensembl and NCBIGene as well as numerous other public and commercial analysis tools. We are currently waiting for the generation of stable microRNA identifiers which we will then use to create microRNA annotations through the application of GO terms.
We are manually capturing protein-protein interaction (PPI) experimental data from the cardiovascular-related literature and submitting this to the IntAct public dataset at EBI. This data is then incorporated into the IMEx Consortium dataset. These annotations will contribute to the expansion and development of the existing PPI network and advance our knowledge about protein interactions within the cardiovascular system.
We are currently focusing on re-annotating papers which we had previously identified as including PPI experimental data, during the previous cardiovascular GO annotation Initiative. For example, the interaction between DVL1 and DVL3 described by Kishida et al, 1999, was captured as a GO annotation in 2008. This interaction is now in the IntAct and IMEx datasets and can therefore be included in software creating PPI networks. Detailed information about the annotation process can be found here.
Current PPI annotation projects:
- Cardiac conduction (Ruth)
- Lipid traits (Nancy, Mila)
- Telomers (Nancy)
- Wnt signalling (Anna)
- Heart development (Mila)
Annotation progress can be viewed either using this link or using the IntAct browser, with the advanced fields search option and selecting from 2 drop down menus field: dataset, cardiac. These approaches both retrieve a list of interactions, which can either be downloaded or viewed using the graph tab.
Our additional PPIs have improved the networks available for individual proteins, for example the number of PPIs associated with ABCA1 has increased by 30%, from 11 PPIs to 15.
We are manually annotating proteins thought or known to play a role in cardiovascular systems through the application of Gene Ontology (GO) terms. Information about the annotation process can be found here. The advantage of a process-focused annotation approach is that it gives the curators time to fully understand the biological area they are annotating and consequently provide highly descriptive annotations. In addition, the curators request very descriptive GO terms, because they are keen to improve the annotation of this domain. Finally each paper is fully annotated, which may not happen when curators are taking a gene product focused approach.
Current GO annotation projects:
Previous GO annotation projects:
- Apoptosis (Ruth)
- Heart development (Varsha, Ruth)
- Insulin signaling (Ruth)
- Lipid metabolism (Ruth)
- Transcription factors associated with heart development (Varsha)
- Heart jogging (Varsha)
- BMP signalling pathway (Varsha)
- Inhibitory SMAD signalling pathway (Varsha)
- Growth factor regulated SMAD signalling pathway (Varsha)
- TGF-beta regulated SMAD signalling pathway (Varsha)
- Inositol 1,4,5-triphosphate-sensitive calcium-release channel pathway (Varsha)
- Growth hormone release pathway (Varsha)
- Reverse cholesterol transport (Ruth)
- Ryanodine-sensitive calcium-release channel activity (Varsha)
- Telomere maintenance (Ruth)
- Transcriptional regulation by TCF7L2 (Ruth)
- Vitamin D metabolism (Varsha)
- Lipid trait risk associated genes (Ruth)
- CAFA2 project list (Anna, Ruth)
We are currently waiting for the generation of stable microRNA identifiers, by RNA central, which we will then use to create microRNA annotations through the application of GO terms. In preparation for the ability to annotate microRNAs we have initiated discussions with other GO Consortium members to establish guidelines to ensure a consistent annotation approach for microRNAs.
Page last modified on 12 mar 14 19:56
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.