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

Arnaiz, Olivier; Cohen, Jean; Tassin, Anne-Marie; Koll, France

doi:10.1186/2046-2530-3-9

Cilia

Table 1 High throughput studies compiled in Cildb V3.0

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

Reference for the study	Method	Species	Ciliary analysis
Andersen et al., 2003 [3]	Centriole proteome	Homo sapiens	yes
Arnaiz et al., 2009 [1]	Cilium proteome	Paramecium tetraurelia	yes
Arnaiz et al., 2010 [7]	Expression during ciliogenesis	Paramecium tetraurelia	yes
Avidor-Reiss et al., 2004 [8]	Comparative genomics	Drosophila melanogaster	yes
Baker et al., 2008a [9]	Spermatozoa proteome	Mus musculus	no
Baker et al., 2008b [10]	Spermatozoa proteome	Rattus norvegicus	no
Bechstedt et al., 2010 [11]	Expression in tissues containing sensory cilia	Drosophila melanogaster	yes
Blacque et al., 2005 [12]	Differential expression between ciliated and non ciliated cells	Caenorhabditis elegans	yes
Blacque et al., 2005 [12]	Genomic screening for X-boxes in promoters	Caenorhabditis elegans	yes
Boesger et al., 2009 [13]	Flagellum phosphoproteome	Chlamydomonas reinhardtii	yes
Broadhead et al., 2006 [14]	Flagellum proteome	Trypanosoma brucei	yes
Cachero et al., 2011 [15]	Expression in early development of future neural cells	Drosophila melanogaster	no
Cao et al., 2006 [16]	Sperm flagellar axonemes proteome	Mus musculus	yes
Chen et al., 2006 [17]	Expression in daf-19 mutant	Caenorhabditis elegans	yes
Datta et al., 2011 [18]	Gene expression with HIPPI expression modulation	Homo sapiens	no
Dorus et al., 2006 [19]	Spermatozoa proteome	Drosophila melanogaster	no
Efimenko et al., 2005 [20]	Genomic screening for X-boxes in promoters	Caenorhabditis elegans	yes
Fritz-Laylin and Cande, 2010 [21]	Flagellum proteome	Naegleria gruberi	yes
Geremek et al., 2011 [22]	Expression in primary ciliary dyskinesia patients	Homo sapiens	yes
Geremek et al., 2014 [23]	Expression in primary ciliary dyskinesia patients	Homo sapiens	yes
Guo et al., 2010 [24]	Proteomics associated with spermiogenesis	Mus musculus	no
Hodges et al., 2011 [25]	Comparative genomics	Chlamydomonas reinhardtii	yes
Hoh et al., 2012 [26]	Expression in multiciliated cells from trachea	Mus musculus	yes
Huang et al., 2008 [27]	Proteomics associated with spermiogenesis	Mus musculus	no
Hughes et al., 2008 [28]	Proteome of Microtubule-Associated Proteins	Drosophila melanogaster	no
Ishikawa et al., 2012 [29]	Primary cilium proteome	Mus musculus	yes
Ivliev et al., 2012 [30]	Expression profile in different tissues	Homo sapiens	yes
Jakobsen et al., 2011 [31]	Centrosome proteomics	Homo sapiens	yes
Keller et al., 2005 [32]	Expression during ciliogenesis	Chlamydomonas reinhardtii	yes
Keller et al., 2005 [32]	Basal body proteome	Chlamydomonas reinhardtii	yes
Kilburn et al., 2007 [33]	Basal body proteome	Tetrahymena thermophila	yes
Kim et al., 2010 [34]	Ciliogenesis modulation	Homo sapiens	yes
Kubo et al., 2008 [35]	Expression in ciliated tissues	Homo sapiens	yes
Laurençon et al., 2007 [36]	Genomic screening for X-boxes in promoters	Drosophila melanogaster	yes
Lauwaet et al., 2011 [37]	Homology search for basal body proteins	Giardia lamblia	yes
Lauwaet et al., 2011 [37]	Basal body proteome	Giardia lamblia	yes
Li et al., 2004 [38]	Comparative genomics	Chlamydomonas reinhardtii	yes
Liu et al., 2007 [39]	Cilium proteome	Mus musculus	yes
Martínez-Heredia et al., 2006 [40]	Spermatozoa proteome	Homo sapiens	no
Mayer et al., 2008 [41]	Cilium proteome	Rattus norvegicus	yes
Mayer et al., 2009 [42]	Cilium proteome	Rattus norvegicus	yes
McClintock et al., 2008 [43]	Expression in ciliated tissues	Mus musculus	yes
Merchant et al., 2007 [44]	Comparative genomics	Chlamydomonas reinhardtii	yes
Müller et al., 2010 [45]	Centrosome proteome	Drosophila melanogaster	yes
Nakachi et al., 2011 [46]	Sperm tail proteome	Ciona intestinalis	yes
Nogales-Cadenas et al., 2009 [47]	Centrosome human curation	Homo sapiens	yes
Ostrowski et al., 2002 [2]	Cilium proteome	Homo sapiens	yes
Pazour et al., 2005 [5]	Expression during ciliogenesis	Chlamydomonas reinhardtii	yes
Pazour et al., 2005 [5]	Flagellum proteome	Chlamydomonas reinhardtii	yes
Phirke et al., 2011 [48]	Down and upregulated genes in daf-19 mutant	Caenorhabditis elegans	yes
Reinders et al., 2006 [49]	Nuclear-associated body proteome	Dictyostelium discoideum	no
Ross et al., 2007 [50]	Expression during ciliogenesis	Homo sapiens	yes
Sakamoto et al., 2008 [51]	Proteome of Microtubule-Associated Proteins	Rattus norvegicus	no
Sauer et al., 2005 [52]	Mitotic spindle proteome	Homo sapiens	no
Smith et al., 2005 [53]	Cilium proteome	Tetrahymena thermophila	yes
Stolc et al., 2005 [54]	Expression during ciliogenesis	Chlamydomonas reinhardtii	yes
Stubbs et al., 2008 [55]	Expression Under FoxJ1 silencing	Xenopus laevis	yes
Wigge et al., 1998 [56]	Spindle pole body proteome	Saccharomyces cerevisiae	no
Yano et al., 2013 [57]	Ciliary membrane proteome	Paramecium tetraurelia	yes

The high throughput studies present in Cildb V3.0 are summarized in thetable with indication in the second column whether it is a proteomic, geneexpression, or genomic study. The species in which the studies have beenperformed are specified in the third column. In the fourth column is thefact whether a given study is ciliary (concerns cilia, flagella, basalbodies, centrioles, centrosomes or spindle pole bodies) or not. The table isordered alphabetically by first author of publication of the studies presentin Cildb V3.0.

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ISSN: 2046-2530

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