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Welcome to Cildb V1

NEW USERS, BEFORE STARTING ANY BIOMART NEW QUERY, PLEASE READ THE HELP TO PROPERLY CHOOSE THE ORTHOLOGY CALCULATION METHOD

YOU ARE WELCOME TO SEE EXAMPLES ON THE QUICK START PAGE IN THE DOCUMENTATION MENU.

Cildb is a knowledgebase, built by the Paramecium Lab at Gif-sur-Yvette, dedicated to proteins involved in centrioles, centrosomes, basal bodies, cilia and flagella in eukaryotes. Cildb contains the whole proteome of 18 species. Orthology relationships between these proteomes have been calculated using Inparanoid ( O'Brien et al., 2005 ) and each relevant protein has been linked to ciliary studies and to human diseases referenced in the OMIM database.

Cildb is also useful for many general searches at the whole genome level, independent of ciliary properties. This is thus a general tool for any researchers (see examples).

The information contained in Cildb is presented as Protein pages that display all orthology and ciliary information, in addition to general attributes such as molecular weigh and isoelectric point of the protein and links to the OMIM data, directly for human proteins or via homology to human proteins for all other species.

The main way to enter Cildb is the use of an Advanced Query tool that uses the BioMart software ( Kasprzyk et al., 2004). Proteins can be filtered according to all kinds of attributes (protein ID, general properties, orthology, ciliary studies, OMIM links).

Cildb can also be entered through a BLAST search, whose output can be visualized as a Biomart table with desired attributes.

Finally, a Gbrowse view of the human genome has been developed in which ciliary properties have been integrated, as well as OMIM entries, even when the feature is not precisely attributed to a gene, but localized to a chromosome region.

The 18 species of Cildb are :

  • the 9 species in which 21 ciliary studies altogether, from 17 publications, have been performed (Homo sapiens, Rattus norvegicus, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Trypanosoma brucei, Chalmydomonas reinhardtii, Paramecium tetraurelia, Tetrahymena thermophila).
  • 4 species because they are good models for ciliary experiments although no study is yet published (Danio rerio, Giardia lamblia, Ciona intestinalis, Plasmodium falciparum)
  • and 5 species because they lack cilia and centrioles, thus represent 'negative controls' in comparative genomics experiments (Arabidopsis thaliana, Dictyostelium discoideum, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Escherichia coli).

Please cite Cildb:

Arnaiz et al. 2009. Cildb: a knowledgebase for centrosomes and cilia Database (2009) Vol. 2009:bap022; doi:10.1093. link