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Resource:Phylogenetic Clusters of Orthologous Groups Ranking

Name: Resource:Phylogenetic Clusters of Orthologous Groups Ranking
Description:

The COG-database has become a powerful tool in the field of comparative genomics. The construction of this data-base is based on sequence homologies of proteins from different completely sequenced genomes. Highly homologous proteins are assigned to clusters of orthologous groups. The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for functional annotation of newly sequenced genomes, including those of complex eukaryotes, and genome-wide evolutionary studies.
The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies.
Here is a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted) proteins encoded in 66 genomes of unicellular organisms.
The eukaryotic orthologous groups (KOGs) include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens), one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe), and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or approximately 54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs.

Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of approximately 20% of the KOG set. This conserved portion of the KOG set is much greater than the ubiquitous portion of the COG set (approximately 1% of the COGs). In part, this difference is probably due to the small number of included eukaryotic genomes, but it could also reflect the relative compactness of eukaryotes as a clade and the greater evolutionary stability of eukaryotic genomes.
Other Name(s): PCOGR
Parent Organization: NIH
Resource Type(s): Database
Resource: Resource
URL: http://www.uni-wh.de/pcogr
Id: nif-0000-21313
Keywords: elegans, encephalitozoon, eukaryote, evolutionary, fly, fruit, fungus, gene, general genomics databases, animal, arabidopsis, caenorhabditis, cerevisiae, classification, comparative, cuniculi, drosophila, genome, genomic, homo, homology, intracellular, melanogaster, microsporidian, nematode, organism, ortholog, orthologous, parasite, pattern, phyletic, phylogenetic, plant, pombe, prokaryote, protein, saccharomyces, sapiens, schizosaccharomyces, sequence, thaliana, tool, unicellular
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CurationStatusuncurated  +
DefiningCitationhttp://www.uni-wh.de/pcogr  +
Definition

The COG-database has become a powe
The COG-database has become a powerful tool in the field of comparative genomics. The construction of this data-base is based on sequence homologies of proteins from different completely sequenced genomes. Highly homologous proteins are assigned to clusters of orthologous groups. The updated collection of orthologous protein sets for prokaryotes and eukaryotes is expected to be a useful platform for functional annotation of newly sequenced genomes, including those of complex eukaryotes, and genome-wide evolutionary studies.
The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies.
Here is a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted) proteins encoded in 66 genomes of unicellular organisms.
The eukaryotic orthologous groups (KOGs) include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens), one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe), and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or approximately 54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs.

Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of approximately 20% of the KOG set. This conserved portion of the KOG set is much greater than the ubiquitous portion of the COG set (approximately 1% of the COGs). In part, this difference is probably due to the small number of included eukaryotic genomes, but it could also reflect the relative compactness of eukaryotes as a clade and the greater evolutionary stability of eukaryotic genomes.
ary stability of eukaryotic genomes.
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +
Idnif-0000-21313  +
Is part ofNIH  +
KeywordsElegans  +, Encephalitozoon  +, Eukaryote  +, Evolutionary  +, Fly  +, Fruit  +, Fungus  +, Gene  +, General genomics databases  +, Animal  +, Arabidopsis  +, Caenorhabditis  +, Cerevisiae  +, Classification  +, Comparative  +, Cuniculi  +, Drosophila  +, Genome  +, Genomic  +, Homo  +, Homology  +, Intracellular  +, Melanogaster  +, Microsporidian  +, Nematode  +, Organism  +, Ortholog  +, Orthologous  +, Parasite  +, Pattern  +, Phyletic  +, Phylogenetic  +, Plant  +, Pombe  +, Prokaryote  +, Protein  +, Saccharomyces  +, Sapiens  +, Schizosaccharomyces  +, Sequence  +, Thaliana  +, Tool  +, and Unicellular  +
LabelResource:Phylogenetic Clusters of Orthologous Groups Ranking  +
ModifiedDate20 June 2013  +
Page has default formThis property is a special property in this wiki.Resource  +
SuperCategoryResource  +
SynonymPCOGR  +