The use of Cildb is to generate lists of proteins, from any of the 44 species included, according to properties that can be chosen and to the desired display. See the quick start procedure.

The properties that can be filtered are ordered in 4 categories:

  • General properties:
    • Name (search in the fields protein ID, gene ID, synonyms, note of the selected species by putting a '%' for 'any character' before and after the keyword)
    • Keywords (same fields as precedent except that the search is extended to all orthologous proteins from all species; put a '%' for 'any character' before and after the keyword)
    • Number of transmembrane helices to look for membrane proteins (put a number)
    • Encoding compartment (nucleus, mitochondrion, chloroplast)
    • Number of ciliary evidences (number of occurrences in ciliary studies, either the protein itself in studies in its organism or in ciliary studies in other species for its orthologs)
    • IN H. SAPIENS ONLY: Chromosome number, start and end to look for a particular region of the human genome
  • Orthology:
    • Has orthologs in one of several of the 43 other species of the database (yes/no)
  • Ciliary evidences
    • For each of the 15 species in which ciliary studies have been performed
      one can filter the number of ciliary evidences in that species
      one can filter the fact that it has been detected in a particular study (yes/no)
  • OMIM
    • Presence of the protein (if in H. sapiens) or of its human ortholog (if in another species) in the OMIM database that links human genetics to diseases (yes/no)
    • Presence in the MORBID database, a subset of OMIM specific for diseases (yes/no)
    • OMIM Keywords allows a text search in the whole OMIM, gene IDs, keywords and description (put a '%' for 'any character' before and after the keyword)

The attributes that can be displayed are the same as the properties that can be filtered, with more details:

  • General properties (For the chosen species- Cildb Accession Number (a unique ID)
    • Protein name
    • Synonyms
    • Note (description)
    • Gene name (important to display in case of alternative splicing: one gene -> several proteins)
    • Encoding Comparment
    • Protein length
    • Isoelectric point
    • Molecular weight
    • Number of transmembrane helices
    • Signal peptide probability
    • Protein sequence
  • Ortholog properties (for the 43 other species)
    • [species_name] ortholog candidates (yes/no)
    • [species_name] ortholog names
    • [species_name] ortholog synonymes
    • [species_name] inparanoid group (a particular Cildb ID specific to each ortholg group between pairs of species: links to an inparlog page)
    • [species_name] inparanoid score (higher with better alignments)
  • Ciliary properties (for each of the 15 species concerned)
    • Number of ciliary evidences in all species (for the protein and its orthologs)
    • Number of organisms with ciliary evidences, since several ciliary studies can come from the same species
    • Number of ciliary evidences in the species
    • Ciliary evidence stringency in the species (the best value if found in several studies; from 1=low to 3=high stringency)
  • Ciliary Studies (only for the species chosen for the search if there are studies) Details for each study according to its type: number of peptides in proteomics, fold change in expression, etc. as well as the stringency concerning the protein
  • OMIM properties (for H. sapiens proteins or for human orthologs in case of other species
    • In OMIM (yes/no)
    • In MORBID (yes/no)
    • OMIM number
    • OMIM title
    • OMIM disorder