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Ciliary studies

Origin of the data

All high throughput studies concerning centriole, centrosome, basal body, cilium or flagellum proteome, available in February 2010, have been retrieved from the original papers and raw results (number of peptides in proteomics, fold change in transcriptome analyses, etc.) have been linked to the protein sequence of the genome version used.

The table below shows the species from which ciliary studies were retreived, the type of study, and the source of original data in the articles. The grey background indicates studies, which are non strictly ciliary thus not included in the counts for ciliary studies in the BioMart query interface.

Articles Year Organism Cilia/Flagella proteome Basal body/centriole/MTOC proteome Expression X-box/rfX Comparative genomics Centrosome proteins, compilation Mitotic spindle proteome Microtubule-associated proteome Sperm cell whole proteome
Andersen et al. 2003Hsapiens
Table S1







Arnaiz et al. 2009PtetraureliaTable S2








Arnaiz et al. 2010Ptetraurelia

-






Avidor-Reiss et al. 2004Dmelanogaster



Table S1




Backer et al. 2008Mmusculus







Table S2
Backer et al. 2008Rnorvegicus







Table S3
Blacque et al. 2005Celegans

Table S1

Table S4




Boesger et al. 2009CreinhardtiiTable S1








Broadhead et al. 2006TbruceiTable S1








Cao et al. 2006MmusculusTable S1








Chen et al. 2006Celegans

Table S3






Dorus et al. 2006Dmelanogaster







Table S1
Efimenko et al. 2005Celegans


Table S1





Huang et al. 2008Mmusculus







Sup. Mat. 05
Hughes et al. 2008Dmelanogaster






Table S1

Keller et al. 2005Creinhardtii
Table S2
Table S4






Kilburn et al. 2007Tthermophila
Table 1







Kim et al. 2010Hsapiens

Table S2






Kubo et al. 2008Hsapiens

Table S1






Laurencon et al. 2007Dmelanogaster


Table3, Table S1





Li et al. 2004Creinhardtii



Table S1




Liu et al. 2007MmusculusTable S1








Martinez-Heredia et al. 2008Hsapiens







Table 1
Mayer et al. 2008RnorvegicusTable 1








Mayer et al. 2009RnorvegicusTable S2








McClintock et al. 2008Mmusculus

Table 1






Merchant et al. 2007Creinhardtii



Table S2




Müller et al. 2010Dmelanogaster
Table S1







Nogales-Cadenas et al. 2006Hsapiens




centrosome:db



Ostrowski et al. 2002HsapiensTable 1, Table 2, Table 1S








Pazour et al. 2005CreinhardtiiTable S1, Table S2

Table S1






Reinders et al. 2006Ddiscoideum
Table 3







Ross et al. 2007Hsapiens

Table S1






Sakamoto et al. 2008Rnorvegicus






Table1

Sauer et al. 2005Hsapiens





Table S1


Smith et al. 2005TthermophilaTable 1S








Stolc et al. 2005Creinhardtii

Table 3






Stubbs et al. 2008Xlaevis

Table S1






Wigge et al. 1998Scerevisiae
Table 1








Definition of confidence thresholds

In each ciliary study, detailed information from raw data has been kept (number of peptides in proteomics, fold change in mRNA in expression experiments, score and distance from ATG in X-box searches, etc.). For regular searches using the Biomart query of Cildb, we have classified the data with 3 confidence thresholds, defined for each study, as shown in the table. This information appears in the filters and attributes as 'low, medium and high confidence'. Otherwise, advanced search allows to filter the data according to the raw values.


Ciliary study Genome / version Method Source Criteria for low confidence Criteria for medium confidence Criteria for high confidence
Blacque et al 2005Celegans WS120 X-box in promoters Table S4dist ≤ or 1500 score ≥ 10dist ≤ 250 or score ≥ 11dist ≤ 100 or score ≥ 12
Blacque et al. 2005Celegans WS120 Differential expression in ciliated tissues Table S1Fold Change ≥ 1.75Fold Change ≥ 2.5Fold Change ≥ 5
Chen et al 2006Celegans WS150 Down regulation in daf19 Table S3Fold Change ≥ 1.75Fold Change ≥ 2.5Fold Change ≥ 5
Efimenko et al 2005Celegans WS122 X-box in promoters Table S1dist ≤ 1000 or nb_mis ≥ 2dist ≤ 250 or nb_mis ≥ 1dist ≤ 100 or nb_mis = 0
Boesger et al 2009Creinhardtii v3 Flagelum phosphoproteome Table S1Rank #1Rank #2Rank #3
Keller et al 2005Creinhardtii v2 Basal body proteome Table S2Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Keller et al 2005Creinhardtii v2 Induction of expression at deflagellation Table S4Fold Change ≥ 1.75Fold Change ≥ 2.5Fold Change ≥ 5
Li et al 2004Creinhardtii v2 Comparative genomics Table S1E-value ≤ 1e-10E-value ≤ 1e-20E-value ≤ 1e-30
Merchant et al 2007Creinhardtii v3 Comparative genomics Table S2All ciliacut specificAll ciliacut specificAll ciliacut specific
Pazour et al 2005Creinhardtii v2 Flagellum proteome Table S1, Table S2Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Pazour et al 2005Creinhardtii v2 Induction of expression at deflagellation Table S1Fold Change ≥ 1.75Fold Change ≥ 2.5Fold Change ≥ 5
Stolc et al 2005Creinhardtii v2 Induction of expression at deflagellation Table 3Fold Change ≥ 1.75Fold Change ≥ 2.5Fold Change ≥ 5
Reinders et al 2006Ddiscoideum Oct 2004 Centrosome proteome Table 3Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Avidor-Reiss et al 2004Dmelanogaster FB v3 Comparative genomics Table S1Rank #1Rank #2Rank #3
Dorus et al 2006Dmelanogaster FB 2006 Sperm cell proteome Table S1Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Hughes et al 2008Dmelanogaster FB 2008 MAPs proteome Table S1Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Laurencon et al 2007Dmelanogaster FB 3.2.1 X-box in promoters Table3, Table S1Rank #1Rank #2Rank #3
Müller et al 2010Dmelanogaster FB 5.30 Mitotic centrosome proteome Table S1Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Andersen et al 2003Hsapiens IPI 2003 Centrosome proteome Table S1Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Kim et al 2010Hsapiens Ambion siRNA library V3.1 Ciliogenesis modulation by RNAi Table S2Rank #1Rank #2Rank #3
Kubo et al 2008Hsapiens Unigene 2008 Differential expression in ciliated tissues Table S1Fold Change ≥ 1.75Fold Change ≥ 2.5Fold Change ≥ 5
Martinez-Heredia et al 2006Hsapiens UniProt 2006 Sperm cell proteome Table 1Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Nogales-Cadenas et al 2006Hsapiens EnsEMBL 2006 Centrosome proteome compilation centrosome:dbAll centrosome:db proteinsAll centrosome:db proteinsAll centrosome:db proteins
Ostrowski et al 2002Hsapiens in house database Cilium proteome Table 1, Table 2, Table 1SNb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Ross et al 2007Hsapiens 37.55 Expression during mucociliary differentiation Table S1Fold Change ≥ 1.75Fold Change ≥ 2.5Fold Change ≥ 5
Sauer et al 2005Hsapiens UniProt 2005 Mitotic spindle proteome Table1Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Backer et al 2008Mmusculus IPI 2008 Sperm cell proteome Table S2Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Cao et al 2006Mmusculus GenBank 2006 Sperm flagellar axoneme proteome Table S1Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Huang et al 2008Mmusculus IPI 2008 Differential proteome in spermatogenesis Sup. Mat. 05Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Liu et al 2007Mmusculus GenBank 2007 Photoreceptor sensory cilium proteome Table S1Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
McClintock et al 2008Mmusculus EnsEMBL 2008 Differential expression in ciliated tissues Table 1Fold Change ≥ 1.75Fold Change ≥ 2.5Fold Change ≥ 5
Arnaiz et al 2009Ptetraurelia 1.0 Cilium proteome Table S2Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Arnaiz et al in prep.Ptetraurelia 1.0 Induction of expression after deciliation -FDR ≤ 0.1FDR ≤ 0.05FDR ≤ 0.01
Backer et al 2008Rnorvegicus IPI 2008 Sperm cell proteome Table S3Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Mayer et al 2008Rnorvegicus GenBank 2007 Olfactory sensory cilium proteome Table 1Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Mayer et al 2009Rnorvegicus GenBank 2009 Olfactory sensory cilium proteome Table S2Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Sakamoto et al 2008Rnorvegicus UniProt 2008 MAPs proteome Table1Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Wigge et al 1998Scerevisiae SGD 1998 Spindle pole proteome Table 1Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Kilburn et al 2007Tthermophila Preliminary release Basal body proteome Table 1Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Smith et al 2005Tthermophila Oct 2007 Cilium proteome Table 1SNb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Broadhead et al 2005Tbrucei v2006 Flagellum proteome Table S1Nb peptides ≥ 1Nb peptides ≥ 2Nb peptides ≥ 4
Stubbs et al 2008Xlaevis Xenbase 2008 Expression in ectoderm overexpressing FoxJ1 Table S1Fold Change ≥ 1.75Fold Change ≥ 2.5Fold Change ≥ 5

dist : distance from ATG
nb_mis : Number of mismatch from consensus
FDR : False discovery rate

References

Celegans

  • Blacque, O.E. et al. Functional Genomics of the Cilium, a Sensory Organelle. Current Biology 15, 935-941(2005). PMID: 15916950
  • Chen, N. et al. Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics. Genome Biol. 7, R126(2006). PMID: 17187676
  • Efimenko, E. et al. Analysis of xbx genes in C. elegans. Development 132, 1923-1934(2005). PMID: 15790967

Creinhardtii

  • Boesger J et al. Analysis of flagellar phosphoproteins from Chlamydomonas reinhardtii. Eukaryot Cell. 8:922-32(2009). PMID: 19429781
  • Keller, L.C. et al. Proteomic Analysis of Isolated Chlamydomonas Centrioles Reveals Orthologs of Ciliary-Disease Genes. Current Biology 15, 1090-1098(2005). PMID: 15964273
  • Li, J.B. et al. Comparative Genomics Identifies a Flagellar and Basal Body Proteome that Includes the BBS5 Human Disease Gene. Cell 117, 541-552(2004). PMID: 15137946
  • Pazour, G.J. et al. Proteomic analysis of a eukaryotic cilium. J Cell Biol. 170, 103-113(2005). PMID: 15998802
  • Stolc, V. et al. Genome-wide transcriptional analysis of flagellar regeneration in Chlamydomonas reinhardtii identifies orthologs of ciliary disease genes. Proc Natl Acad Sci U S A. 102, 3703-3707(2005). PMID: 15738400
  • Merchant,S.S. et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science, 318, 245-250(2007). PMID: 17932292.

Ddiscoideum

  • Reinders,Y. et al. Identification of novel centrosomal proteins in Dictyostelium discoideum by comparative proteomic approaches. J. Proteome Res, 5, 589-598(2006). PMID: 16512674.

Dmelanogaster

  • Avidor-Reiss, T. et al. Decoding Cilia Function: Defining Specialized Genes Required for Compartmentalized Cilia Biogenesis. Cell 117, 527-539(2004). PMID: 15137945
  • Laurencon, A. et al. Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species. Genome Biol. 8, R195(2007). PMID: 17875208
  • Dorus,S. et al. Genomic and functional evolution of the Drosophila melanogaster sperm proteome. Nat. Genet, 38, 1440-1445(2006). PMID: 17099714.
  • Müller H. et al. Proteomic and functional analysis of the mitotic Drosophila centrosome. EMBO J. 29:3344-3357(2010). PMID: 20818332
  • Hughes,J.R. et al. A microtubule interactome: complexes with roles in cell cycle and mitosis. PLoS Biol, 6, e98(2008). PMID: 18433294.

Hsapiens

  • Andersen, J.S. et al. Proteomic characterization of the human centrosome by protein correlation profiling. Nature 426, 570-574(2003). PMID: 14654843
  • Ostrowski, L.E. et al. A Proteomic Analysis of Human Cilia: Identification of Novel Components. Mol Cell Proteomics 1, 451-465(2002). PMID: 12169685
  • Kim J. et al. Functional genomic screen for modulators of ciliogenesis and cilium length. Nature 464:1048-51(2010). PMID: 20393563
  • Kubo,A. et al. Sentan: a novel specific component of the apical structure of vertebrate motile cilia. Mol. Biol. Cell, 19, 5338-5346(2008). PMID: 18829862.
  • Martínez-Heredia,J. et al. Proteomic identification of human sperm proteins. Proteomics, 6, 4356-4369(2006). PMID: 16819732.
  • Nogales-Cadenas,R. et al. CentrosomeDB: a human centrosomal proteins database. Nucleic Acids Res, 37, D175-80(2006). PMID: 18971254.
  • Ross,A.J. et al. Transcriptional profiling of mucociliary differentiation in human airway epithelial cells. Am. J. Respir. Cell Mol. Biol, 37, 169-185(2007). PMID: 17413031.
  • Sauer,G. et al. Proteome analysis of the human mitotic spindle . Mol. Cell Proteomics, 4, 35-43(2005). PMID: 15561729.

Mmusculus

  • Liu, Q. et al. The Proteome of the Mouse Photoreceptor Sensory Cilium Complex. Mol Cell Proteomics. 6, 1299-317(2007). PMID: 17494944
  • Baker,M.A. et al. The mous sperm proteome characterized via IPG strip prefractionation and LC-MS/MS identification. Proteomics, Apr;8(8):1720-30 (2008). PMID: 18340633.
  • Cao,W. et al. Proteomic profiling of accessory structures from the mouse sperm flagellum. Mol. Cell Proteomics, 5, 801-810(2006). PMID: 16452089.
  • Huang,X. et al. Construction of a proteome profile and functional analysis of the proteins involved in the initiation of mouse spermatogenesis. J. Proteome Res, 7, 3435-3446(2008). PMID: 18582094.
  • McClintock,T.S. et al. Tissue expression patterns identify mouse cilia genes. Physiol. Genomics, 32, 198-206(2008). PMID: 17971504.

Ptetraurelia

  • Arnaiz,O. et al. Cildb: a knowledgebase for centrosomes and cilia. Database Vol. 2009:bap022; doi:10.1093(2009). PMID: 20428338
  • Arnaiz,O. et al. Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia BMC Genomics 11:547(2010) PMID: 20932287

Rnorvegicus

  • Mayer, U. et al. Proteomic Analysis of a Membrane Preparation from Rat Olfactory Sensory Cilia. Chem. Senses 33, 145-162(2008). PMID: 18032372
  • Mayer U. et al. The proteome of rat olfactory sensory cilia. Proteomics 9:322-34(2009). PMID: 19086097
  • Baker,M.A. et al. The rat sperm proteome characterized via IPG strip prefractionation and LC-MS/MS identification. Proteomics, 8, 2312-2321(2008). PMID: 18528845.
  • Sakamoto,T. et al. Mass spectrometric analysis of microtubule co-sedimented proteins from rat brain. Genes Cells, 13, 295-312(2008). PMID: 18363962.

Scerevisiae

  • Wigge,P.A. et al. Analysis of the Saccharomyces spindle pole by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. J. Cell Biol, 141, 967-977(1998). PMID: 9585415.

Tbrucei

  • Broadhead, R. et al. Flagellar motility is required for the viability of the bloodstream trypanosome. Nature 440, 224-227(2006). PMID: 16525475

Tthermophila

  • Kilburn, C.L. et al. New Tetrahymena basal body protein components identify basal body domain structure. J Cell Biol. 178, 905-912(2007). PMID: 17785518
  • Smith, J. et al. Robust Method for Proteome Analysis by MS/MS Using an Entire Translated Genome: Demonstration on the Ciliome of Tetrahymena thermophila. J. Proteome Res. 4, 909-919(2005). PMID: 15952738

Xlaevis

  • Stubbs,J.L. et al. The forkhead protein Foxj1 specifies node-like cilia in Xenopus and zebrafish embryos. Nat. Genet, 40, 1454-1460(2008). PMID: 19011629.