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Welcome to Cildb V2.1

NEW USERS, BEFORE STARTING ANY BIOMART NEW QUERY, PLEASE READ THE HELP PAGE 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. The version 2.1 of Cildb contains the whole proteomes of 33 species. Orthology relationships between these proteomes have been calculated using Inparanoid (O'Brien et al., 2005) and each relevant protein has been linked to high throughput ciliary studies and to human diseases referenced in the OMIM database (October 2010).

Cildb is also useful for many general searches at the whole genome level, independent of ciliary properties. (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). Subtractive genomics queries are also possible in Cildb 2.1.

Cildb can also be entered through a BLAST search or Motif search, whose outputs 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 33 species of Cildb version 2.1 are :

  • 26 centric species, i.e. with cilia/flagella or at least centrioles at some stage of their life cycle, including:
    • The 10 species in which 32 high throughput ciliary studies altogether, from 28 publications, have been performed (Homo sapiens, Rattus norvegicus, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Trypanosoma brucei, Chalmydomonas reinhardtii, Paramecium tetraurelia, Tetrahymena thermophila and Xenopus laevis).
    • 16 other species because they are good models for ciliary experiments although no high throughput study is yet published (Batrachochytrium dendrobatidis, Chlorella sp_NC64A, Ciona intestinalis, Danio rerio, Giardia lamblia, Micromonas sp, Monosiga brevicollis, Naegleria gruberi, Ostreococcus lucimarinus, Physcomitrella patens, Plasmodium falciparum, Selaginella moellendorffii, Schmidtea mediterrannea, Thalassiosira pseudonana, Toxoplasma gondii and Trichoplax adhaerens).
  • 7 acentric species because they lack cilia and centrioles, thus represent 'negative controls' in comparative genomics experiments including:
    • 2 species for which 2 analyses on centrosome and spindle pole proteomes are available in (Dictyostelium discoideum and Saccharomyces cerevisiae).
    • 5 species without particular relevant studies (Arabidopsis thaliana, Escherichia coli, Phaeodactylum tricornutum, Podospora anserina, Schizosaccharomyces pombeand Dictyostelium discoideum.

Related studies, not strictly concerning ciliary/centrosomal have also been incorporated into Cildb:

  • 2 studies on microtubule associated proteins (Drosophila melanogaster, Rattus norvegicus)
  • 1 study on the mitotic spindle proteome (Homo sapiens )
  • 5 studies on the proteome of whole sperm cells, in which the flagellum is an important contributor (Homo sapiens, Rattus norvegicus, Mus musculus, Drosophila melanogaster)

Changes compared to Cildb V1

Please cite Cildb:

Arnaiz et al. 2009. Cildb: a knowledgebase for centrosomes and cilia Database (2009) Vol. 2009:bap022; doi:10.1093. link PMID: 20428338