Ciliated species are denoted as: C. elegans (Ce), C. reinhardtii (Cr), D. melanogaster (Dm), H. sapiens (Hs), M. musculus (Mm), P. falciparum (Pf), T. brucei (Tb), and non-ciliated species: A. thaliana (At), D. discoideum (Dd), S. cerevisiae (Sc). Proteomics method is indicated by: comparative genomics (CG), mass spectrometry (MS), transcriptional profiling during flagellar regeneration (TXN), analysis of genes containing an x-box (XBX).
      The ciliary proteome database consists of different subsets: generated by either non-reciprocal or reciprocal BLAST. To build the non-reciprocal database set, we used BLAST to find human orthologs for all reported ciliary proteins. Only the best hit (with the most statistically significant alignment) was taken, with a maximum Expect (E) value of e-10. These proteins were then sorted into different cutoff groups: e-10, e-20, and e-30 (See table below). We then constructed the reciprocal database set by first utilizing BLAST to find human orthologs for all reported ciliary proteins. Only the best hit was taken, with a maximum Expect (E) value of e-10. We then carried out reciprocal BLAST by aligning the best hit human ortholog to the proteins from the original species where that protein was identified. If the best reciprocal hit corresponds to the genomic coordinates encoding the original protein, the protein is retained in the dataset. If not, the protein is not included in the reciprocal database. We used UniProt v12.5 for all protein sequence data except Chlamydomonas, for which protein sequences were taken from ChlamyDB version 2.

Study
Method
Organism
Original source of proteins
Comments
Total proteins
Human orthologs
Reciprocal
Non-reciprocal
e-10
e-20
e-30
e-10
e-20
e-30
Li et al. 2004
CG
 Chlamydomonas reinhardtii Supplementary Table S1 All
688
226
155
97
376
219
145
Efimenko et al. 2005
XBX
 Caenorhabditis elegans Supplementary Table S1 Position <= 1000, Homology score => 12
395
21
20
17
295
254
213
Stolc et al. 2005
TXN
 Chlamydomonas reinhardtii Supplementary Table 9 All
220
79
67
55
103
82
65
Ostrowski et al. 2002
MS
 Homo sapiens Table II Identified by => 2 peptides, or 1 peptide if the protein was reported in another study.
165
112
109
107
112
109
107
Pazour et al. 2005
MS
 Chlamydomonas reinhardtii Supplementary Table S1 All
652
182
156
133
269
215
175
Avidor-Reiss et al. 2004
CG
 Drosophila melanogaster Supplementary Table S1 All
183
141
130
113
166
155
135
Keller et al. 2005
MS
 Chlamydomonas reinhardtii Supplementary Table 2 All proteins except contaminants in peak basal body fraction
129
44
39
36
55
48
43
Andersen et al. 2003
MS
 Homo sapiens Supplementary Table A All centrosome, centrosome candidates, and centrosome novel proteins identified by => 2 peptides, or 1 peptide if the protein was reported in another study.
110
104
101
100
104
101
100
Blacque et al. 2005
XBX
 Caenorhabditis elegans Supplementary Table S4 Position <= 1000, Homology score => 12
396
173
154
138
320
270
230
Broadhead et al. 2006
MS
 Trypanosoma brucei Supplemental Figure 1 All proteins with pI < 10.2
326
74
58
47
123
88
68
Liu et al. 2007
MS
 Mus musculus Supplemental Table S1 All proteins from Worksheet "A - PSC Complex Proteome"
1925
1730
1729
1726
1855
1848
1843

      Above images: (A and B) Whole genome subtraction of ciliated from non-ciliated organisms was reported by Avidor-Reiss et al. (2004) and Li et al. (2004) respectively. Images reproduced from Nature publishing (Drosophila), Max Planck Institute of Molecular Plant Physiology (Arabidopsis), Art of color (Vitruvian man). (C) Human bronchial epithelial cilia were analyzed by MS. Image cropped from Figure 1A, (Ostrowski et al. 2002). (D) Novel human centrosomal proteins were validated by expressing green fluorescent protein (GFP) fusion proteins in U2OS cells. The merged GFP (green) with gamma-tubulin centrosomal marker (red) indicates centrosomal localization. Image reproduced from Figure 2A (Andersen et al. 2002). (E) The mouse photoreceptor sensory cilium (PSC) proteome was defined in both wild-type and rootletin null photoreceptors. A rootletin knockout PSC preparation is shown with rootletin stained in red and RP1 stained in green. Image adapted from Figure 2J (Liu et al. 2007). (F and G) C. elegans genes responsible for ciliogenesis were elucidated by a genome-wide search for genes with an x-box upstream regulatory motif (Efimenko et al. 2005; Blacque et al. 2005 respectively). Cross-section of amphid sensory cilia (F) reproduced from wormatlas.org. (G) Cilia-related candidate genes were experimentally verified with GFP tags in vivo. Image reproduced from Figure 1 (Blacque et al. 2005) (H) Trypanosome flagellar proteins were analyzed by MS. Image adapted from Landfear (2006), Figure 1A. (I) Genes related to ciliary generation are upregulated upon flagellar amputation of Chlamydomonas and was catalogued by Stolc et al. (2005). Electron micrograph of deflagellated C. reinhardtii by Ursula Goodenough (Washington University, St. Louis, MO). (J and K) MS was employed to elucidate the Chlamydomonas centriole (Keller et al. 2005) and flagellar (Pazour et al. 2005) proteomes respectively. Scanning micrograph of a C. reinhardtii centriole (J) cropped from Figure 2H (Fromherz et al. 2004). C. reinhardtii image (K) provided by Rudiger Schmitt (Regensburg University, Regensburg, Germany).