ChlamyFPv5
The Chlamydomonas Flagellar Proteome Project
Proteomic Data Sets
CrFP Total Peptides (Pazour et al. Witman 2005)
Wang Peptides (Wang et al. Pan 2017)
Jordan Peptides (Jordan et al. Pigino 2018)(Total Unique Peptides)
Picariello Peptides (Picariello et al. Witman 2019)(Total Unique Peptides)
Zhao Central Apparatus Project (Zhao et al. Witman 2019)(Total Unique Peptides, summed from two biological replicates for each. Proteins found only in this dataset needed 10 or more peptides to be included)
Dai Central Apparatus Project (Dai et al. Bui 2019)
Developmental Changes in Ciliary Composition during Gametogenesis in Chlamydomonas (Sakato-Antoku and King 2022)(Normalized Total Spectra of all proteins already in CrFP, proteins listed in Table 1, and proteins that had at least 10 spectra in the total dataset)
Genome Assembly
The Chlamydomonas genome reveals the evolution of key animal and plant functions. (Merchant et al. Grossman 2007)
The Chlamydomonas Genome Project, version 6: reference assemblies for mating type plus and minus strains reveal extensive structural mutation in the laboratory. (Craig et al.Merchant 2022)
Gene Expression Data Sets
Fold Upregulated Post Deflagellation (Albee et al. Dutcher 2013)
Importance of XAP5 for expression (Li et al. Hu 2018); also see (PNAS Editors 2021)
Evalues
Homo sapiens (Hs taxids 9606) (Refseq top BLAST E value and gene name)
Mus musculus (Mm taxids 10090) (Refseq top BLAST E value and gene name)
Gonium pectorale (Gp taxids 33097) (NR top BLAST E value)
Hofstenia miamia (Hm taxids 442651) (top BLAST E value)
Caenorhabditis elegans (Ce taxids 6239) (NR top BLAST E value)
Drosophila melanogaster (Dm taxids 7227) (NR top BLAST E value)
Plasmodium falciparum (Pf taxids 5833) (NR top BLAST E value)
Trypanosoma brucei (Tb taxids 5691) (NR top BLAST E value)
Arabidopsis thaliana (At taxids 3702) (NR top BLAST E value)
Saccharomyces cerevisiae (Sc taxids 4932) (NR top BLAST E value)
Phospho Proteomic Data Sets
Investigating the effect of target of rapamycin kinase inhibition on the Chlamydomonas reinhardtii phosphoproteome: from known homologs to new targets. (Werth et al. Hicks 2018)
Pazour unpublished, reanalysis of phosphopeptides from 2005 dataset.
Protein phosphorylation is a key event of flagellar disassembly revealed by analysis of flagellar phosphoproteins during flagellar shortening in Chlamydomonas. (Pan et al. Hippler 2011)
FLA8/KIF3B phosphorylation regulates kinesin-II interaction with IFT-B to control IFT entry and turnaround. (Liang et al. Pan 2014)
Identification and Characterization of Components of the Intraflagellar transport (IFT) Machinery: a Dissertation. (Yuqing Hou Thesis)
Analysis of flagellar phosphoproteins from Chlamydomonas reinhardtii. (Boesger et al. Mittag 2009)
The global phosphoproteome of Chlamydomonas reinhardtii reveals complex organellar phosphorylation in the flagella and thylakoid membrane. (Wang et al. Hicks 2014)
Label-Free Quantitative Phosphoproteomics for Algae. (Ford et al. Hicks 2020)
Confidence:
High: Four or more peptides in the CrFP or published support for a role in ciliary biology. Histones and ribosomal proteins were moved out of this class.
Medium: Two to four peptides in the CrFP or a publication linking an orthologue to ciliary biology.
Weak: One peptide in the CrFP or found in one of the other proteomes that I included. Currently no papers to support ciliary association.
Zero: Things that are included for historical reasons but currently have no support for being ciliary associated.
Human Disease Genes
Default is top BLAST match if better than 1e-10
Data from papers that specifically searched for orthologs takes precedence
• A Unified Taxonomy for Ciliary Dyneins (Hom et al. King 2011 PMID 21953912)
• The unity and diversity of the ciliary central apparatus (Zhao et al. Witman 2020 PMID 31884923)
• Data from individual papers was used when available.
Human diseases started from published papers
• The genetic landscape of cardiovascular left-right patterning defects (Wells et al. Ware 2022 PMID 35777348)
• The Joubert-Meckel-Nephronophthisis Spectrum of Ciliopathies. (Van De Weghe et al. Doherty 2022 PMID 35655331)
• Genes and molecular pathways underpinning ciliopathies. (Reiter et al. Leroux 2017 PMID 28698599)
• Data from individual papers was used when available.