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CiliaCarta: An integrated and validated compendium of ciliary genes
- Source :
- PLoS ONE, PLoS One, 14, PLoS One. Public Library of Science, PloS one, PLOS ONE, PLOS ONE, 14(5):0216705. Public Library of Science, PLoS ONE, Vol 14, Iss 5, p e0216705 (2019), PLoS One, 14, 5
- Publication Year :
- 2019
- Publisher :
- Public Library of Science, 2019.
-
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/. This work was supported by the European Community’s Seventh Framework Programme [241955, 278568 to MU and KB, 602273 to RS]; the Virgo consortium, funded by the Dutch government [FES0908 to TvD, RvdL and MAH]; the Netherlands Genomics Initiative [050-060-452 to TvD, RvdL and MAH]; the Canadian Institutes of Health Research [MOP-142243, MOP-82870 and PJT-156042 to MRL]; Michael Smith Foundation for Health Research to MRL and VLJ; Kidney Research Scientist Core Education and National Training fellowship to VLJ; The Foundation Fighting Blindness [PPA-0717-0719-RAD to UW, RR, and MU]; the Dutch Kidney Foundation “KOUNCIL” consortium [CP11.18 to RHG, PLB and RR]; The Deutsche Forschungsgemeinschaft [Excellence grant CellNetworks to RBR and QL, CRC1140 “Kidney Disease – From Genes to Mechanisms” to MS, collaborative research center grant SFB-1411 KIDGEM to MS]; Metakids Foundation to RS; the National Institute for Health Research to PLB and VH-H. PLB is an NIHR Senior Investigator; Radboudumc Hypatia Tenure Track Fellowship, Radboud Universiteit excellence fellowship, ERC starting grant TREATCilia, grant agreement no. 716344 to MS; and the Netherlands Organization for Scientific Research [NWO Vici-865.12.005 to RR].
- Subjects :
- Proteomics
Sensory Receptors
Nematoda
Social Sciences
Ciliopathies
Biochemistry
Sensory disorders Donders Center for Medical Neuroscience [Radboudumc 12]
Transcriptome
0302 clinical medicine
Animal Cells
Psychology
RETINAL PHOTORECEPTOR CELLS
Exome
Neurons
0303 health sciences
030302 biochemistry & molecular biology
Eukaryota
Genomics
PRIMARY CILIUM
thecilium
3. Good health
Nucleic acids
Genetic interference
Osteichthyes
Medicine
Epigenetics
Cellular Structures and Organelles
Cellular Types
proteomic databases
Sensory Receptor Cells
Science
education
Ciliary genes
LEBER CONGENITAL AMAUROSIS
03 medical and health sciences
Genetics
Cilia
Caenorhabditis elegans
IDENTIFICATION
MUTATIONS
Embryos
cilia
Organisms
Biology and Life Sciences
Bayes Theorem
Molecular Sequence Annotation
medicine.disease
Invertebrates
Fish
ciliary proteome
Animal Studies
Caenorhabditis
Gene expression
embryos
030217 neurology & neurosurgery
Developmental Biology
Neuroscience
Photoreceptors
Candidate gene
Embryology
Oligonucleotides
Morpholino
Database and Informatics Methods
RNA interference
Bayesian classifier
TRANSITION ZONE
Zebrafish
Antisense Oligonucleotides
Multidisciplinary
Spectrometric Identification of Proteins
Proteomic Databases
Nucleotides
Cilium
Stable Isotope Labeling by Amino Acids in Cell Culture
photoreceptors
Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6]
Animal Models
Phenotype
INTRAFLAGELLAR TRANSPORT
DIFFERENTIATION
Experimental Organism Systems
Caenorhabditis Elegans
Vertebrates
Sensory Perception
Research Article
Signal Transduction
EXPRESSION
Stable isotope labeling by amino acids in cell culture
Computational biology
Biology
Research and Analysis Methods
SOLUTE-CARRIER-PROTEIN
Model Organisms
medicine
Animals
data integration
030304 developmental biology
Afferent Neurons
Reproducibility of Results
Cell Biology
zebrafish
biology.organism_classification
Ciliopathy
Renal disorders Radboud Institute for Molecular Life Sciences [Radboudumc 11]
Biological Databases
Cellular Neuroscience
RNA
OSCP1
CiliaCarta
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 14
- Issue :
- 5
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....2772a70100890267dc91fbed9c4e654e