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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 
<http://cildb.cgm.cnrs-gif.fr/v3/page/quick_start> procedure.

Cildb is a knowledgebase, built by the Paramecium Lab 
<http://www.cgm.cnrs-gif.fr/spip.php?article180> 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 <http://cildb.cgm.cnrs-gif.fr/v3/cgi/genome_versions>. 
Orthology relationships <http://cildb.cgm.cnrs-gif.fr/v3/cgi/orthology> 
between these proteomes have been calculated using Inparanoid 
<http://inparanoid.sbc.su.se/cgi-bin/index.cgi> (O'Brien et al., 2005 
<http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=15608241>) 
and each relevant protein has been linked to high throughput ciliary 
studies <http://cildb.cgm.cnrs-gif.fr/v3/cgi/ciliary_studies> and to 
human diseases referenced in the OMIM database 
<http://www.ncbi.nlm.nih.gov/omim/> (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 
<http://cildb.cgm.cnrs-gif.fr/v3/page/about> 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 
<http://cildb.cgm.cnrs-gif.fr/martexplorer/#%21/default?mart=Cildb> tool 
that uses the BioMart software <http://www.biomart.org/> (Kasprzyk et 
al., 2004 
<http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=14707178>). 
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 
<http://cildb.cgm.cnrs-gif.fr/v3/page/blast> search or Motif search 
<http://cildb.cgm.cnrs-gif.fr/v3/cgi/patmatdb>, whose outputs can be 
visualized as a Biomart table with desired attributes.

Finally, a Gbrowse view <http://cildb.cgm.cnrs-gif.fr/v3/gb2/gbrowse> 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 <http://cildb.cgm.cnrs-gif.fr/v3/cgi/genome_versions> 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:
      o The 15 species in which 55 high throughput ciliary studies
        <http://cildb.cgm.cnrs-gif.fr/v3/cgi/ciliary_studies>
        altogether, from 52 publications
        <http://cildb.cgm.cnrs-gif.fr/v3/page/references>, 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/).
      o 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:
      o 2 species for which 2 analyses on centrosome and spindle pole
        proteomes are available in (/Dictyostelium discoideum/ and
        /Saccharomyces cerevisiae/).
      o 7 species without particular relevant studies (/Arabidopsis
        thaliana, Escherichia coli, Phaeodactylum tricornutum, Laccaria
        bicolor, Mortierella verticillata, Podospora anserina,
        Schizosaccharomyces pombe/and /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 
<http://cildb.cgm.cnrs-gif.fr/v3/cgi/ciliary_studies> from 9 
publications <http://cildb.cgm.cnrs-gif.fr/v3/page/references>) :

  * 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 
<http://cildb.cgm.cnrs-gif.fr/v3/page/versions>


      Please cite Cildb:

*Arnaiz et al.* 2009. Cildb: a knowledgebase for centrosomes and cilia 
*Database* (2009) Vol. 2009:bap022; doi:10.1093. link 
<http://database.oxfordjournals.org/cgi/content/short/2009/0/bap022?rss=1> 
PMID: 20428338 <http://www.ncbi.nlm.nih.gov/pubmed/20428338>

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


    Versions


      Version 3.0 - July 2014 <http://cildb.cgm.cnrs-gif.fr/v3/page/index>

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
      <http://cildb-archive.cgm.cnrs-gif.fr/v2/page/index>

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
      <http://cildb-archive.cgm.cnrs-gif.fr/v1/page/index>

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/
>>>>>>>>