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)

Human Axonemes (Gui et al. Brown 2022)

Bovine Doublets (Gui et al. Brown 2021)

Human Respiratory Cilia (Blackburn et al. Ostrowski 2017)

Frog Motile Cilia (Sim et al. Kwon 2020)

Human Sperm Flagella (Baker et al. Aitken 2013)

Mouse Sperm Flagella (Zhou et al. Wu 2023)

Human Sperm Flagella (Zhou et al. Wu 2023)

Human Sperm Flagella (Amaral et al. Oliva 2013)

Shinde Arl6 Apex (Shinde et al. Nachury 2023)

Protein Atlas (Karlson et al. 2022)

SysCilia Gold List (Vasquez et al. Wheway 2021)

Cilia Carta (van Dam et al. Huynen 2019)

Ishikawa Primary Cilia (Ishikawa et al Marshall 2012)

Mick Primary Cilia Apex (Mick et al. Nachury 2015)

May Primary Cilia Apex2 (May et al. Mick 2021)

Mick Ift27 Primary Cilia Apex (Mick et al. Nachury 2015)

Breslow CRISPR Hedgehog Signaling (Breslow et al. Nachury 2018)

Pusapati CRISPR Hedgehog Signaling (Pusapati et al. Rohagti 2018)

Hoh 4 and 12 day ALI (Hoh et al. Stearns 2012)

Mouse Sperm Flagella (Tai et al. Zhu 2023)

Bovine Sperm Centrioles (Firat-Karalar et al. Stearns 2014)

HEK Cell Centrosome (Carden et al. Gergely 2023)

Gene Names, Loci, and Descriptions are from Wormbase.

Human Homologs. Only the top hit is shown. There may be other homologs that are relevant.

Mammalian Annotation

Human Diseases as curated by (Disease Ontology Org), Retnet, and others

WormCat: An Online Tool for Annotation and Visualization of Caenorhabditis elegans Genome-Scale Data (Holdorf et al. Walker 2020).

Ou : Ivermectin Resistance

Piecing together a proteome (Inglis et al. Leroux 2006). If an entry is shown, the gene was in this dataset

Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport (Phirke et al Swoboda 2011 ). DAF-19 regulated genes; fold change with negative numbers being down regulated

Whole-Organism Developmental Expression Profiling Identifies RAB-28 as a Novel Ciliary GTPase Associated with the BBSome and Intraflagellar Transport (Jensen et al Blacque 2021). Values better than the authors cutoff are shown.

Identification of ciliary and ciliopathy genes in Caenorhabditis elegans through comparative genomics (Chen et al Stein 2006). Genes with conserved X-box sequences.

A phylogenetic profiling approach identifies novel ciliogenesis genes in Drosophila and C. elegans (Dobbelaere et al. Dammermann 2023 ). If an entry is shown the gene was in this datase.

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)

Fold Upregulated Post Deflagellation (Albee et al. Dutcher 2013)

Importance of XAP5 for expression (Li et al. Hu 2018); also see (PNAS Editors 2021)

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)

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)

Application of phosphoproteomics to find targets of casein kinase 1 in the flagellum of chlamydomonas. (Boesger et al. Mittag 2012)

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)

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.