CiliaCarta: An integrated and validated compendium of ciliary genes
van Dam, T.J.P.; Kennedy, Julie E.; van der Lee, Robin; De Vrieze, Erik; Wunderlich, Kirsten A.; Rix, Suzanne; Dougherty, Gerard; Lambacher, Nils J.; Li, Chunmei; Jensen, Victor L; Leroux, Michel R.; Hjeij, Rim; Horn, Nicola; Texier, Yves; Wissinger, Yasmin; Van Reeuwijk, Jeroen; Wheway, Gabrielle; Knapp, Barbara; Scheel, Jan F.; Franco, Brunella; Mans, Dorus A.; Van Wijk, Erwin; Kepes, François; Slaats, Gisela G.; Toedt, Grischa; Kremer, Hannie; Omran, Heymut; Szymanska, Katarzyna; Koutroumpas, Konstantinos; Ueffing, Marius; Nguyen, Thanh Minh T.; Letteboer, Stef J.F.; Oud, Machteld M.; Van Beersum, Sylvia E.C.; Schmidts, Miriam; Beales, Philip L; Lu, Qianhao; Giles, Rachel H.; Szklarczyk, Radek; Russell, Robert B.; Gibson, Toby J.; Johnson, Colin A.; Blacque, Oliver E.; Wolfrum, Uwe; Boldt, Karsten; Roepman, Ronald; Hernandez-Hernandez, Victor; Huynen, Martijn H.
(2019) PLoS One
(Article)
Abstract
The cilium is an essential organelle at the surface of most mammalian cells whose dysfunction causes a wide range of genetic diseases collectively called ciliopathies. The current rate at which new ciliopathy genes are identified suggests that many ciliary components remain undiscovered. We generated and rigorously analyzed genomic, proteomic, transcriptomic
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and evolutionary data and systematically integrated these using Bayesian statistics into a predictive score for ciliary function. This resulted in 285 candidate ciliary genes. We found experimental evidence of ciliary associations for 24 out of 36 analyzed candidate proteins. In addition, we show that OSCP1, which has previously been implicated in two distinct non-ciliary functions, causes a cilium dysfunction phenotype when depleted in zebrafish. The candidate list forms the basis of CiliaCarta, a comprehensive ciliary compendium covering 836 genes. The resource can be used to objectively prioritize candidate genes in whole exome or genome sequencing of ciliopathy patients and can be accessed at http://bioinformatics.bio.uu.nl/john/syscilia/ciliacarta/.
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Keywords: Ciliary genes, thecilium, Bayesian classifier, CiliaCarta, OSCP1, ciliary proteome, data integration
ISSN: 1932-6203
Publisher: Public Library of Science
(Peer reviewed)
