New users, please see the quick start procedure.
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. Compared to previous versions, the version 3.1 of Cildb contains more species proteomes and more High throughput ciliary studies. Its interface has been simplified using the novel version 9 of Biomart. Cildb V3.0 contains the whole proteomes of 44 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 (June 2014).
Cildb is also useful for many general searches at the whole genome level, independent of ciliary properties.
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 Search tool that uses the BioMart software (Kasprzyk et al., 2004). Proteins can be filtered according to all kinds of properties (protein ID, general properties, orthology, ciliary studies, OMIM links).
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 44 species of Cildb version 3.0 are :
- 32 centric species, i.e. with cilia/flagella or at least centrioles at some stage of their life cycle, including:
- The 15 species in which 55 high throughput ciliary studies altogether, from
52 publications, have been performed
( Caenorhabditis elegans, Chalmydomonas reinhardtii, Ciona intestinalis, Drosophila melanogaster, Giardia lamblia, Homo sapiens, Mus musculus, Naegleria gruberi, Paramecium tetraurelia, Rattus norvegicus, Schmidtea mediterrannea,
Tetrahymena thermophila, Trypanosoma brucei and Xenopus laevis).
- 17 other species because they are good models for ciliary experiments although no high throughput study is yet published (Allomyces macrogynus, Apis mellifera, Batrachochytrium dendrobatidis, Chlorella sp_NC64A, Danio rerio, Emiliana huxleyi, Micromonas sp, Monosiga brevicollis, Ostreococcus tauri, Physcomitrella patens, Phytophtora infestans, Plasmodium falciparum, Selaginella moellendorffii, Spizellopyces punctatus, Thalassiosira pseudonana, Toxoplasma gondii and Trichoplax adhaerens).
- The 15 species in which 55 high throughput ciliary studies altogether, from 52 publications, have been performed ( Caenorhabditis elegans, Chalmydomonas reinhardtii, Ciona intestinalis, Drosophila melanogaster, Giardia lamblia, Homo sapiens, Mus musculus, Naegleria gruberi, Paramecium tetraurelia, Rattus norvegicus, Schmidtea mediterrannea, Tetrahymena thermophila, Trypanosoma brucei and Xenopus laevis).
- 9 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).
- 7 species without particular relevant studies (Arabidopsis thaliana, Escherichia coli, Phaeodactylum tricornutum, Laccaria bicolor, Mortierella verticillata, Podospora anserina, Schizosaccharomyces pombeand Dictyostelium discoideum.
- 3 prokaryote species because they resemble ancestors of symbiotic organelles : mitochondria (Rickettsia prowazekii) and chloroplasts (Synechocystis sp PCC6803, Chlamydia pneumoniae)
Related studies, not strictly concerning ciliary/centrosomal have also been incorporated into Cildb (11 studies from 9 publications) :
- 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)
- 1 study on the expression during development of future neural cells in early development ( Drosophila melanogaster)
- 1 study on Gene expression in context of HIPPI overexpression or silencing in HeLa cells of ( Homo sapiens)
- 1 study on RNAi screen on Hh and Wnt pathways in ( Mus musculus)
Please cite Cildb:
Arnaiz O, Cohen J, Tassin AM, Koll F. Remodeling Cildb, a popular database for
cilia and links for ciliopathies.
Cilia. 2014 2014 Nov 17;3:9. doi:10.1186/2046-2530-3-9. eCollection 2014. link PMID: 25422781
Arnaiz O, Malinowska A, Klotz C, Sperling L, Dadlez M, Koll F, Cohen J. Cildb:
a knowledgebase for centrosomes and cilia.
Database (Oxford). 2009 Vol. 2009:bap022. doi:10.1093. link PMID: 20428338