PUBLICATION
Representing Kidney Development Using the Gene Ontology
- Authors
- Alam-Faruque, Y., Hill, D.P., Dimmer, E.C., Harris, M.A., Foulger, R.E., Tweedie, S., Attrill, H., Howe, D.G., Thomas, S.R., Davidson, D., Woolf, A.S., Blake, J.A., Mungall, C.J., O'Donovan, C., Apweiler, R., Huntley, R.P.
- ID
- ZDB-PUB-140619-3
- Date
- 2014
- Source
- PLoS One 9: e99864 (Journal)
- Registered Authors
- Howe, Doug
- Keywords
- none
- MeSH Terms
-
- Animals
- Databases, Genetic
- Databases, Protein
- Gene Ontology*
- Humans
- Kidney/embryology*
- Kidney/metabolism*
- Mice
- Molecular Sequence Annotation
- Species Specificity
- Statistics as Topic
- PubMed
- 24941002 Full text @ PLoS One
Citation
Alam-Faruque, Y., Hill, D.P., Dimmer, E.C., Harris, M.A., Foulger, R.E., Tweedie, S., Attrill, H., Howe, D.G., Thomas, S.R., Davidson, D., Woolf, A.S., Blake, J.A., Mungall, C.J., O'Donovan, C., Apweiler, R., Huntley, R.P. (2014) Representing Kidney Development Using the Gene Ontology. PLoS One. 9:e99864.
Abstract
Gene Ontology (GO) provides dynamic controlled vocabularies to aid in the description of the functional biological attributes and subcellular locations of gene products from all taxonomic groups (www.geneontology.org). Here we describe collaboration between the renal biomedical research community and the GO Consortium to improve the quality and quantity of GO terms describing renal development. In the associated annotation activity, the new and revised terms were associated with gene products involved in renal development and function. This project resulted in a total of 522 GO terms being added to the ontology and the creation of approximately 9,600 kidney-related GO term associations to 940 UniProt Knowledgebase (UniProtKB) entries, covering 66 taxonomic groups. We demonstrate the impact of these improvements on the interpretation of GO term analyses performed on genes differentially expressed in kidney glomeruli affected by diabetic nephropathy. In summary, we have produced a resource that can be utilized in the interpretation of data from small- and large-scale experiments investigating molecular mechanisms of kidney function and development and thereby help towards alleviating renal disease.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping