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)
- Telomeres (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:
- Cardiac conduction (Ruth)
- Telomerase and telomere-related proteins (Nancy)
- Proteins involved in miRNA processing (Rachael)
- Folic acid metabolism (Hadil Alrohaif, MSc project student)
- Hereditary hemochromatosis (Klaus Mitchell, MSc project student)
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)
News April 2015
We are pleased to announce our first release of Gene Ontology (GO) annotations describing the biological roles of microRNAs (miRNAs).
Previously, we have concentrated on providing annotations to proteins and, more recently, macromolecular complexes. In November we began a project to curate miRNAs that are involved with cardiovascular development and related processes. In conjunction with this effort we have curated the roles of the key human proteins that are involved in miRNA processing, such as Drosha and Dicer.
The RNA annotations are available in the regular GOA release files (available from ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/) and in AmiGO2. For example see the annotations associated with hsa-miR-133a. These annotations will shortly be available in the new version of QuickGO.
There are currently around 80
annotations provided by the UCL team to RNAcentral identifiers, but this is due
to increase substantially as the project progresses.
Furthermore, we have circulated microRNA annotation guidelines to other GO Consortium members, to ensure a consistent annotation approach for microRNAs. These have been generally accepted and will soon be circulated to microRNA experts.
Please address any queries to Rachael Huntley, the lead biocurator for this project.
Decision Tree of the GO terms and annotation extensions used for capturing targets of miRNAs.
The types of evidence are listed in the blue boxes. The green boxes summarise the data supporting the data available and the annotations that can therefore be generated. The pink boxes indicate that the published descriptions of an miRNA does not meet the GOC guideline criteria will not be captured.
A reporter assay, or a Co-IP plus an assay demonstrating an effect of the miRNA on mRNA levels, is sufficient to classify a target as “validated binding”, additional evidence that the target is predicted for the miRNA does not affect the annotation given therefore this option is not shown. Author justification means the author indicates why this mRNA is an expected target or shows an effect on an expected downstream process.
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.