CiliaCarta: a validated compendium of ciliary genes

About the CiliaCarta

Welcome to the CiliaCarta. This webpage was created to provide easy access and search capabilities to researchers interesting in using our predictions. For detailed information please contact John van Dam.

The CiliaCarta is based on a naive Bayesian integration of a diverse set of data sets to predict novel ciliary genes. Each data set has been evaluated for its propensity to retrieve known ciliary genes and than integrated using Bayes' theorem. The CiliaCarta Score is a log transformed odds which means that a positive score indicates that a gene is more likely to be ciliary than not ciliary.

On this webpage we provide two tables:

  1. The CiliaCarta as the compendium of ciliary genes, comprising our previous SYSCILIA Gold Standard resource, Gene Ontology annotated genes and our top predictions which have been validated experimentally.
  2. The naive Bayesian integration, including all datasets used in the analysis. A proteome wide list providing probabilities for each individual gene.

The selected data can directly be downloaded as a plain text *.csv file or as an excel *.xlsx file.

Contents of CiliaCarta

Figure: Venn diagram summarizing the contents of CiliaCarta.

Citation

If you are using the CiliaCarta in your research please consider citing our paper:

We are in the process of peer review of our manuscript. A version of our manuscript can be found on the pre-print server bioRxiv:

van Dam, T. J. P. et al. CiliaCarta: An Integrated And Validated Compendium Of Ciliary Genes. bioRxiv 123455 (2017). doi:10.1101/123455

The supplementary figures and tables belonging to the bioRxiv manuscript can be downloaded here.

Please visit this page again at a later time for updated citation information, or contact either John or Martijn. It would be much appreciated!

Note that we have updated this website (March 21 2018) to include recent Gene Ontology annotations. You can find the old version here.

Contact

Dr. TJP (John) van Dam
Email: t.j.p.vandam-at-uu.nl

Theoretical Biology and Bioinformatics
Utrecht University
Padualaan 8
3584 CH, Utrecht
The Netherlands

Prof. Dr. Martijn A Huynen
Email: Martijn.Huijnen-at-radboudumc.nl

CMBI, RIMLS, Radboud university medical centre
Geert Grooteplein 26-28, route 260
PO Box 9101
6500 HB Nijmegen
The Netherlands

Centre for Molecular and Biomolecular Informatics    Radboud Institute for Molecular Life Sciences    Radboud University Medical Center, Nijmegen    Utrecht University    Utrecht Bioinformatics Center    VIRGO    SYSCILIA logo    Framework 7 Project    EU   


Ensembl Gene ID Associated Gene Name Description CiliaCarta Rank CiliaCarta Score Inclusion criterion
Ensembl Gene ID Associated Gene Name Description CiliaCarta Rank CiliaCarta Score Inclusion criterion

The column 'group' denotes if a gene belonged to the positive training set (P), the negative training set (N), or unknown (G for ‘grey’). Thus in our set with an cFDR value of 25%, the 'grey' genes are our predictions for novel ciliary genes.

Ensembl Gene ID Associated Gene Name Description Group Gene Ontology CiliaCarta Rank CiliaCarta Score cFDR TAP PPI SILAC PPI Mass-Spec based PPI Y2H PPI RFX/FOXJ1 TFBS Cilia co-occurrence Expression screen Liu_2007 (CilDB) Ross_2007 (CilDB)
Ensembl Gene ID Associated Gene Name Description Group Gene Ontology CiliaCarta Rank CiliaCarta Score cFDR TAP PPI SILAC PPI Mass-Spec based PPI Y2H PPI RFX/FOXJ1 TFBS Cilia co-occurrence Expression screen Liu_2007 (CilDB) Ross_2007 (CilDB)

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Funding

SYSCILIA logoFramework 7 Project   EU The European Community's Seventh Framework Programme FP7/2009, grant agreement number 241955, SYSCILIA

VIRGO The Virgo consortium, funded by the Dutch government (FES0908), and by the Netherlands Genomics Initiative (050-060-452).

UBC The Utrecht Bioinformatics Center, Utrecht University.