The Gene Ontology of eukaryotic cilia and flagella
By Paola Roncaglia, Teunis J. P. van Dam, Karen R. Christie, L. Nacheva, Grischa Toedt, Martijn A. Huynen, Rachael P. Huntley, Toby J. Gibson, Jane Lomax. 2017
8 citations recorded by the source corpus.
BackgroundRecent research into ciliary structure and function provides important insights into inherited diseases termed ciliopathies and other cilia-related disorders. This wealth of knowledge needs to be translated into a computational representation to be fully exploitable by the research community. To this end, members of the Gene Ontology (GO) and SYSCILIA Consortia have worked together to improve representation of ciliary substructures and processes in GO.MethodsMembers of the SYSCILIA and Gene Ontology Consortia suggested additions and changes to GO, to reflect new knowledge in the field. The project initially aimed to improve coverage of ciliary parts, and was then broadened to cilia-related biological processes. Discussions were documented in a public tracker. We engaged the broader cilia community via direct consultation and by referring to the literature. Ontology updates were implemented via ontology editing tools.ResultsSo far, we have created or modified 127 GO terms representing parts and processes related to eukaryotic cilia/flagella or prokaryotic flagella. A growing number of biological pathways are known to involve cilia, and we continue to incorporate this knowledge in GO. The resulting expansion in GO allows more precise representation of experimentally derived knowledge, and SYSCILIA and GO biocurators have created 199 annotations to 50 human ciliary proteins. The revised ontology was also used to curate mouse proteins in a collaborative project. The revised GO and annotations, used in comparative ‘before and after’ analyses of representative ciliary datasets, improve enrichment results significantly.ConclusionsOur work has resulted in a broader and deeper coverage of ciliary composition and function. These improvements in ontology and protein annotation will benefit all users of GO enrichment analysis tools, as well as the ciliary research community, in areas ranging from microscopy image annotation to interpretation of high-throughput studies. We welcome feedback to further enhance the representation of cilia biology in GO.
Subfields: Cellular and Molecular Neuroscience, Genetics, Pulmonary and Respiratory Medicine
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Citations in the corpus
- The Gene Ontology Resource: 20 years and still GOing strong (2018, background): “Recent examples include cilium biology (7,8), autophagy (9) and cardiac phenotypes (10).”
- Sensing the cilium, digital capture of ciliary data for comparative genomics investigations (2018, methodology): “…term ‘cilium’ (purple arrows) as well as the previously discussed term, ‘photoreceptor connecting cilium’ (dark green arrows), have much more significant p values in the December 2016 data, as was also observed during enrichment analysis of the entire human SCGS gene set in Rongaglia et al. [8].”