van Dam, Teunis J. P., Kennedy, Julie, van der Lee, Robin ORCID: 0000-0001-7391-9438, de Vrieze, Erik ORCID: 0000-0003-3448-3269, Wunderlich, Kirsten A., Rix, Suzanne, Dougherty, Gerard W., Lambacher, Nils J., Li, Chunmei, Jensen, Victor L., Leroux, Michel R., Hjeij, Rim, Horn, Nicola, Texier, Yves, Wissinger, Yasmin, van Reeuwijk, Jeroen, Wheway, Gabrielle ORCID: 0000-0002-0494-0783, Knapp, Barbara, Scheel, Jan F., Franco, Brunella, Mans, Dorus A., van Wijk, Erwin, Kepes, Francois, Slaats, Gisela G., Toedt, Grischa, Kremer, Hannie ORCID: 0000-0002-0841-8693, 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 ORCID: 0000-0002-1714-6749, 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 ORCID: 0000-0002-5178-8163, Hernandez-Hernandez, Victor and Huynen, Martijn A. (2019). CiliaCarta: An integrated and validated compendium of ciliary genes. PLoS One, 14 (5). SAN FRANCISCO: PUBLIC LIBRARY SCIENCE. ISSN 1932-6203

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Abstract

The cilium is an essential organelle at the surface of 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 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 generated independent experimental evidence of ciliary associations for 24 out of 36 analyzed candidate proteins using multiple cell and animal model systems (mouse, zebrafish and nematode) and techniques. For example, we show that OSCP1, which has previously been implicated in two distinct non-ciliary processes, causes ciliogenic and ciliopathy-associated tissue phenotypes when depleted in zebrafish. The candidate list forms the basis of CiliaCarta, a comprehensive ciliary compendium covering 956 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/.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
van Dam, Teunis J. P.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kennedy, JulieUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
van der Lee, RobinUNSPECIFIEDorcid.org/0000-0001-7391-9438UNSPECIFIED
de Vrieze, ErikUNSPECIFIEDorcid.org/0000-0003-3448-3269UNSPECIFIED
Wunderlich, Kirsten A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Rix, SuzanneUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Dougherty, Gerard W.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lambacher, Nils J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Li, ChunmeiUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Jensen, Victor L.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Leroux, Michel R.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Hjeij, RimUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Horn, NicolaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Texier, YvesUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wissinger, YasminUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
van Reeuwijk, JeroenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wheway, GabrielleUNSPECIFIEDorcid.org/0000-0002-0494-0783UNSPECIFIED
Knapp, BarbaraUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Scheel, Jan F.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Franco, BrunellaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Mans, Dorus A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
van Wijk, ErwinUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kepes, FrancoisUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Slaats, Gisela G.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Toedt, GrischaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Kremer, HannieUNSPECIFIEDorcid.org/0000-0002-0841-8693UNSPECIFIED
Omran, HeymutUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Szymanska, KatarzynaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Koutroumpas, KonstantinosUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Ueffing, MariusUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Nguyen, Thanh-Minh T.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Letteboer, Stef J. F.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Oud, Machteld M.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
van Beersum, Sylvia E. C.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Schmidts, MiriamUNSPECIFIEDorcid.org/0000-0002-1714-6749UNSPECIFIED
Beales, Philip L.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Lu, QianhaoUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Giles, Rachel H.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Szklarczyk, RadekUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Russell, Robert B.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gibson, Toby J.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Johnson, Colin A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Blacque, Oliver E.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Wolfrum, UweUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Boldt, KarstenUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Roepman, RonaldUNSPECIFIEDorcid.org/0000-0002-5178-8163UNSPECIFIED
Hernandez-Hernandez, VictorUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Huynen, Martijn A.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-148150
DOI: 10.1371/journal.pone.0216705
Journal or Publication Title: PLoS One
Volume: 14
Number: 5
Date: 2019
Publisher: PUBLIC LIBRARY SCIENCE
Place of Publication: SAN FRANCISCO
ISSN: 1932-6203
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
RETINAL PHOTORECEPTOR CELLS; LEBER CONGENITAL AMAUROSIS; SOLUTE-CARRIER-PROTEIN; PRIMARY CILIUM; INTRAFLAGELLAR TRANSPORT; TRANSITION ZONE; EXPRESSION; MUTATIONS; DIFFERENTIATION; IDENTIFICATIONMultiple languages
Multidisciplinary SciencesMultiple languages
Refereed: Yes
URI: http://kups.ub.uni-koeln.de/id/eprint/14815

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