Clusters of Orthologous Groups (COGs): Difference between revisions
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Browsing the COG database is easy, as there are links everywhere. However, there is no explanation as to what is on the links. | |||
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Revision as of 05:21, 10 July 2006
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| Clusters of Orthologous Groups (COGs) | |
| Who: | NCBI |
| What: | Phylogenetic classification of proteins encoded in complete genomes |
| Where: | Clusters of Orthologous Groups (COGs) |
| Updates | |
| Upcoming events | link to event calendar, if applicable |
| Web Services | |
About Clusters of Orthologous Groups (COGs)
The Clusters of Orthologous Groups (COGs) of proteins were generated by comparing the protein sequences of complete genomes. Each cluster contains proteins or groups of paralogs from at least three lineages. The current COG database contains both prokaryotic clusters (COGs) and eukaryotic clusters (KOGs).
Content
The COGs database contains Clusters from both Unicellular and Eukaryotic Organisms. There are currently 66 Unicellular organisms and can be found here. The eukaryotic organisms are limited to seven organisms: Arabidopsis thaliana, Caenorhabditis elegans, Drosophilia melanogaster, Homo Sapiens, Saccharomyces cerevisiae, Schizosaccharomyces pombe and Encephalitozoon cuniculi.
The following statistics come from Tatusov RL et al (2003).
The COG collection consists of 138,458 proteins from 66 genomes. These proteins form 4873 COGs. Unfortunatly, these COGs are not available on the website. Howewver, a subset are available from the initial version. The KOG sets contain 4,852 clusters of orthologs, utilizing 59,838 proteins. This is approximately 54% of the analyzed eukaryotic gene products.
Categories
The COGs and KOGs are classified into functional classifications. The functional categories are not listed on the newe version of the COG website. They are designated in the paper and listed below for reference.
| A | RNA processing and modification |
| B | Chromatin Structure and dynamics |
| C | Energy production and conversion |
| D | Cell cycle control and mitosis |
| E | Amino Acid metabolis and transport |
| F | Nucleotide metabolism and transport |
| G | Carbohydrate metabolism and transport |
| H | Coenzyme metabolis |
| I | Lipid metabolism |
| J | Tranlsation |
| K | Transcription |
| L | Replication and repair |
| M | Cell wall/membrane/envelop biogenesis |
| N | Cell motility |
| O | Post-translational modification, protein turnover, chaperone functions |
| P | Inorganic ion transport and metabolism |
| Q | Secondary Structure |
| T | Signal Transduction |
| U | Intracellular trafficing and secretion |
| Y | Nuclear structure |
| Z | Cytoskeleton |
| R | General Functional Prediction only |
| S | Function Unknown |
Using Clusters of Orthologous Groups (COGs)
It should be noted that the updated version of the COG database does not have functional interactions with COGs. However, the KOG clusters have interaction.
Browsing
Browsing the COG database is easy, as there are links everywhere. However, there is no explanation as to what is on the links.
Searching
Usage examples
Technology
Web Services/API
Discussion
References
The COG database: an updated version includes eukaryotes.
Tatusov RL et al BMC Bioinformatics. 2003 Sep 11;4:41. Epub 2003 Sep 11.
Full Text
The COG database: a tool for genome-scale analysis of protein functions and evolution.
Tatusov RL et al Nucleic Acids Res. 2000 Jan 1;28(1):33-6. Full Text
A genomic perspective on protein families.
Tatusov RL et al Science. 1997 Oct 24;278(5338):631-7.Abstract
External Links
Clusters of Orthologous Groups (COGs)