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. 2014 Nov 17:3:9.
doi: 10.1186/2046-2530-3-9. eCollection 2014.

Remodeling Cildb, a popular database for cilia and links for ciliopathies

Olivier Arnaiz  1 , Jean Cohen  1 , Anne-Marie Tassin  1 , France Koll  1
Affiliations

Remodeling Cildb, a popular database for cilia and links for ciliopathies

Olivier Arnaiz et al. Cilia. .

Abstract

Background: New generation technologies in cell and molecular biology generate large amounts of data hard to exploit for individual proteins. This is particularly true for ciliary and centrosomal research. Cildb is a multi-species knowledgebase gathering high throughput studies, which allows advanced searches to identify proteins involved in centrosome, basal body or cilia biogenesis, composition and function. Combined to localization of genetic diseases on human chromosomes given by OMIM links, candidate ciliopathy proteins can be compiled through Cildb searches.

Methods: Othology between recent versions of the whole proteomes was computed using Inparanoid and ciliary high throughput studies were remapped on these recent versions.

Results: Due to constant evolution of the ciliary and centrosomal field, Cildb has been recently upgraded twice, with new species whole proteomes and new ciliary studies, and the latter version displays a novel BioMart interface, much more intuitive than the previous ones.

Conclusions: This already popular database is designed now for easier use and is up to date in regard to high throughput ciliary studies.

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Figures

Figure 1
Figure 1
The species whose whole proteome has been included into Cildb V3.0 are gathered by taxonomy groups, with indication whether they are centric or not and of the number of high throughput studies, ciliary or not, performed in the species. The choice of species to include into Cildb was 1) species in which high throughput ciliary studies have been performed, 2) species routinely used as models in ciliary studies in general, and 3) centric and acentric species, because the presence/absence of certain proteins may be relevant for the conservation of ciliary proteins through evolution. The case of the Bug22/GTL3/C16orf80 protein, composed of a domain called DUF667, essential for ciliary motility [6], was carefully examined for the choice of fungi to add in Cildb for comparative genomics. Bug22 is a protein highly conserved in all centric species, be they metazoans, protozoa, plants or fungi and curiously also highly conserved in the acentric land plants, but absent from the genomes of higher fungi already sequenced at the time of the publication, i.e. acentric ascomycetes [6]. Owing to constant new genome sequencing, novel fungal whole proteomes appeared and the occurrence of Bug22 was different from what was thought earlier. It is still undetectable in ascomycetes, but is found conserved in the acentric Mortierella verticillata (accession MVEG_01915), and a more divergent Bug22 with recognizable DUF667 domain is found in several basidiomycetes represented in Cildb by Laccaria bicolor (accession 598201). This property was one of the reasons to include those two fungi proteomes into Cildb V3.0. This also emphasizes that constant arrival of new knowledge as new genomes are sequenced can put into questions former assumptions such as the absence of particular proteins in some species, here Bug22 in fungi.
Figure 2
Figure 2
An advanced search on Cildb V3.0 is started by clicking on the ‘Search’ button on the top row on the right. Then, it is necessary to choose the species in which the proteome has to be searched for. The filter window then appears to adjust the filters in the left panel (no filter means that the full proteome will be retrieved). Similarly, the output window allows displaying particular properties (attributes) in columns for each filtered protein. A summary on the right reminds the user of all the filters and attributes currently used. This also allows direct modification of the orders of the columns in the output by moving the attributes up and down in the list. The last operation of the process is to show the results. The results are given by pages of 20 items with a maximum of 1000 items. To see all results, they have to be downloaded as a file. At any time, if the result output seems incomplete or inappropriate, the filters and attributes can be modified by using the ‘Back’ button (edit results) to refine the search and show the results again. The quick search allows a rapid search by keywords. The result can be processed the same way as the one described above, with the possibility to add attributes by ‘Edit results’ and to download the file. Note the direct access to BLAST, Human genome Gbrowse, Motif search, Help and access to older Versions of Cildb on the top row buttons to the right.
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