Print

Print


SORRY FOR ANY DUPLICATE MAIL

Dear all,

This is an anouncement that your preferred ciliary database, Cildb (http://cildb.cgm.cnrs-gif.fr/) is now updated to version 3.0. Below is the copy of the home page, as well as the page indicating the changes to previous versions.

Enjoy it!

All the best
Jean Cohen and Olivier Arnaiz

-------------------------

Welcome to Cildb V3.0



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).
  • 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)

Changes compared to Cildb V2

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

---------------------------------------

Versions

Version 3.0 - July 2014 

Compared to Version 2.1, the Version 3.0 has been significantly remodeled, with more species and studies, but with simplified interface:

  • Eleven novel species whose interest comes from their evolutionary positions and the fact they do or not possess cilia or centrioles. We included the whole proteomes of Allomyces macrogynus, Apis mellifera, Emiliania huxleyi, Laccaria bicolor, Mortierella verticillata, Ostreococcus tauri (in repalcement of Ostreococcus lucimarinus), Phytophtora infestans, Spizellomyces punctatus and Theileria parva .
  • Twenty one new ciliary/centrosomal high throughput studies together with three other non ciliary but related studies.
  • Introduction of the encoding compartment of the proteins. Most of them are encoded by the nucleus in eukaryotes, but we attributed the properties of mitochondrion or chloroplast as encoding compartment both in the filters and display.
  • Update of the links with OMIM (May 2014)

The interface of Cildb V3.0 has been changed to the version 9 of BioMart, which is much more intuitive than previous ones.

  • Due to improvement of the Inparamoid algorithm, we suppressed the in-house homology calculation (filtered best hits) for orthology calculation. There is no orthology choice anymore in the query form.
  • Filters have been simplified for easier queries. However, all the properties of each protein can be diplayed as attributes and sorted in a file after export.


Version 2.1 - October 2010

 

Compared to Version 2.0, the new features of Version 2.1 include:

  • Four new ciliary/centrosomal high throughput studies.
  • Update of the links with OMIM (October 2010)
  • Implementation of a Motif search tool


Version 2.0 - July 2010 

Compared to Version 1.0, the new features of Version 2.0 include:

  • Seven new ciliary/centrosomal high throughput studies.
  • Two new studies from acentriolar species, since the relevant organelles are functionally related to higher cell centrosomes: centrosomes of Dictyostelium discoideum and spindle poles of Saccharomyces cerevisiae.
  • Eight other non ciliary/centrosomal studies have been incorporated: Microtubule-associated proteomes, spindle proteomes and whole sperm cell proteomes of various species.
  • Fifteen novel species whose interest comes from their evolutionary positions and the fact they do or not possess cilia or centrioles. The use of these species will be particularly relevant for comparative genomics. For example, we included the whole proteomes of two diatoms, the acentric Phaeodactylum tricornutum and the centric Thalassiosira pseudonana. This brings up to 33 the number of species in Cildb.
  • Suppression of the Filterd Blastp database as a choice of orthology method in BioMart queries, just keeping Inparanoid and Inparanoid and filtered Best Hit. To perform the subtractive genomics queries previously allowed by the Filterd Blastp database, we included Blast e-values as properties that can be filtered and displayed as attibutes. Subtractive genomics can now be performed by filtering according to e-values in a customized way, using e-value cutoff between 0 and 1.
  • Update of the links with OMIM (May 2010)
  • For users particularly interested in searching candidate genes for partially localized ciliopathies, we added the possibility of filtering the nucleotide positions on Homo Sapiens chromosomes in the BioMart query.


Version 1.0 - December 2008

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.

-- 
<<<<<<<<
Jean Cohen
Centre de Génétique Moléculaire
CNRS, Avenue de la Terrasse
91198 Gif-sur-Yvette cedex, France

Tel +33 (0)169824373
Fax +33(0)169823181
email [log in to unmask]
http://www.cgm.cnrs-gif.fr/spip.php?article180
http://paramecium.cgm.cnrs-gif.fr/
http://cildb.cgm.cnrs-gif.fr/
>>>>>>>>