If rhythmic behavior
is spoiled in mutant animal, but circadian rhythm itself was intact (ex.
rhythmic expression of clock genes and clock controlled genes), the gene cannot be regarded as clock gene.
The gene was defined as a "output gene". Output gene was not listed in the table.
Note, rhythmic expression is one feature of most of "clock
gene", but is not essential nor sufficient. There are hundreds of
rhythmic transcribed "clock-controlled genes (cgg)". Sirt1 was included to the table temporarily. Circadian function of SIRT1was shown in culture cells, but not in animal mutant.
Gene name of human,
mouse, frog and fly was shown according guidelines
for gene nomenclature.
Gene name was italicized except Xenopus according guideline: "Gene names should be in lower
case and not in italics" (Suggested Xenopus Gene Name
Human gene name was shown in upper case according guideline: ex., CLOCK.
Mouse gene name was capitalized according guideline: ex., Clock. Fly gene was shown in a full name or in a common name, if it was simple: ex., clk = clock Branchiostoma,Anopheles, Nematostella and Trichoplax. Gene Symbols were abbreviated: ex., BRAFLDRAFT_63636 = BF_63636.
GB number was used for Apis
mellifera instead of symbol, if the gene was not named.
Gene name was painted as follows.
Red: clock function was reported in animal model. Mutation was found in human sleep disorder.
Yellow: clock function was reported in cultured cell.
Non clock family genes were listed in table for reference.
Protein (deduced gene product) name in BLINK, Cladogram and Phylogram
Protein name was shown in upper case with prefix (or suffix) of abbreviated scientific name: ex., mm_CLOCK.
In phylogenetic analysis, official symbol, synonim and abbreviated name was used: ex., mouse Bhlhe40 product = mm_DEC1.
If the gene name was not decided and the gene product has certain
similarity to known gene, we used the name of the known gene: ex., Apis mellifera GB17107 = am_CLOCK.
Animal species was selected as follows,
For Chordata, one species was selected from each taxonomic Class.
Mammalia. Human and mouse was listed. Human was added for reference.
Amphibia. Xenopus (Silurana) tropicalis and Xenopus laevis were listed. Because genome and EST information of both species are in progress.
For Class Insecta, well characterized three species were listed.
Drosophila melanogaster (fruit fly) and Anopheles gambiae (mosquito) belongs to the same taxonomic Order. Anopheles was added because it has mammalian type cry, which was not found in Drosophila
Genes belong to same Homologene was shown in arbitrary color.
If unknown gene has certain similarity to known gene, Homologene field was paint with same color to the known gene.
Homolog in fungi and plant were listed, if it was listed in Homologene.
While listed in Homologene, mammalian species (chimpanzee, Pan troglodytes; dog, Canis lupus; cattle, Bos taurus; Rat, Rattus norvegicus) were omitted.
Definition of Homolog
Homolog(1) was identified using
using Refseq protein sequence for human or Drosophila gene products as a query.
We also used BLAST service listed in "Tools".
The gene product with highest similarity to query was examined by Blast search against human and Drosophila database.
If the candidate shows the highest similarity to the human or Drosophila query, then the candidate was regarded as the homolog of human or Drosophila gene.
For family genes, the candidate was examined by phylogenetic analysis using ClustalW2.
Homolog in fungi and plant were listed without similarity search, if it was listed in Homologene.