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eggNOG: automated construction and annotation of orthologous groups of genes.

Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P - Nucleic Acids Res. (2007)

Bottom Line: Existing approaches either lack functional annotation of the identified orthologous groups, hampering the interpretation of subsequent results, or are manually annotated and thus lag behind the rapid sequencing of new genomes.We automatically annotated our non-supervised orthologous groups with functional descriptions, which were derived by identifying common denominators for the genes based on their individual textual descriptions, annotated functional categories, and predicted protein domains.The orthologous groups in eggNOG contain 1 241 751 genes and provide at least a broad functional description for 77% of them.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

ABSTRACT
The identification of orthologous genes forms the basis for most comparative genomics studies. Existing approaches either lack functional annotation of the identified orthologous groups, hampering the interpretation of subsequent results, or are manually annotated and thus lag behind the rapid sequencing of new genomes. Here we present the eggNOG database ('evolutionary genealogy of genes: Non-supervised Orthologous Groups'), which contains orthologous groups constructed from Smith-Waterman alignments through identification of reciprocal best matches and triangular linkage clustering. Applying this procedure to 312 bacterial, 26 archaeal and 35 eukaryotic genomes yielded 43 582 course-grained orthologous groups of which 9724 are extended versions of those from the original COG/KOG database. We also constructed more fine-grained groups for selected subsets of organisms, such as the 19 914 mammalian orthologous groups. We automatically annotated our non-supervised orthologous groups with functional descriptions, which were derived by identifying common denominators for the genes based on their individual textual descriptions, annotated functional categories, and predicted protein domains. The orthologous groups in eggNOG contain 1 241 751 genes and provide at least a broad functional description for 77% of them. Users can query the resource for individual genes via a web interface or download the complete set of orthologous groups at http://eggnog.embl.de.

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Screenshot of the main results page. The eggNOG database was queried for the three G1-type cyclins in budding yeast, namely Cln1–Cln3. These have been correctly assigned to two fungal orthologous groups. The navigation tree at the top of the page allows the user to change the view to more coarse-grained orthologous groups, for example the eukaryotic orthologous groups in which these cyclins are all grouped together.
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Figure 2: Screenshot of the main results page. The eggNOG database was queried for the three G1-type cyclins in budding yeast, namely Cln1–Cln3. These have been correctly assigned to two fungal orthologous groups. The navigation tree at the top of the page allows the user to change the view to more coarse-grained orthologous groups, for example the eukaryotic orthologous groups in which these cyclins are all grouped together.

Mentions: Figure 2 shows the result of a query for the three G1-type cyclins in budding yeast, which belong to two distinct fungal orthologous groups. Function descriptions are displayed for both the orthologous groups and for the individual genes. The web interface enables the user to view the complete set of genes that belong to each orthologous group and provides external links to additional information on the protein products.Figure 2.


eggNOG: automated construction and annotation of orthologous groups of genes.

Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P - Nucleic Acids Res. (2007)

Screenshot of the main results page. The eggNOG database was queried for the three G1-type cyclins in budding yeast, namely Cln1–Cln3. These have been correctly assigned to two fungal orthologous groups. The navigation tree at the top of the page allows the user to change the view to more coarse-grained orthologous groups, for example the eukaryotic orthologous groups in which these cyclins are all grouped together.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238944&req=5

Figure 2: Screenshot of the main results page. The eggNOG database was queried for the three G1-type cyclins in budding yeast, namely Cln1–Cln3. These have been correctly assigned to two fungal orthologous groups. The navigation tree at the top of the page allows the user to change the view to more coarse-grained orthologous groups, for example the eukaryotic orthologous groups in which these cyclins are all grouped together.
Mentions: Figure 2 shows the result of a query for the three G1-type cyclins in budding yeast, which belong to two distinct fungal orthologous groups. Function descriptions are displayed for both the orthologous groups and for the individual genes. The web interface enables the user to view the complete set of genes that belong to each orthologous group and provides external links to additional information on the protein products.Figure 2.

Bottom Line: Existing approaches either lack functional annotation of the identified orthologous groups, hampering the interpretation of subsequent results, or are manually annotated and thus lag behind the rapid sequencing of new genomes.We automatically annotated our non-supervised orthologous groups with functional descriptions, which were derived by identifying common denominators for the genes based on their individual textual descriptions, annotated functional categories, and predicted protein domains.The orthologous groups in eggNOG contain 1 241 751 genes and provide at least a broad functional description for 77% of them.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

ABSTRACT
The identification of orthologous genes forms the basis for most comparative genomics studies. Existing approaches either lack functional annotation of the identified orthologous groups, hampering the interpretation of subsequent results, or are manually annotated and thus lag behind the rapid sequencing of new genomes. Here we present the eggNOG database ('evolutionary genealogy of genes: Non-supervised Orthologous Groups'), which contains orthologous groups constructed from Smith-Waterman alignments through identification of reciprocal best matches and triangular linkage clustering. Applying this procedure to 312 bacterial, 26 archaeal and 35 eukaryotic genomes yielded 43 582 course-grained orthologous groups of which 9724 are extended versions of those from the original COG/KOG database. We also constructed more fine-grained groups for selected subsets of organisms, such as the 19 914 mammalian orthologous groups. We automatically annotated our non-supervised orthologous groups with functional descriptions, which were derived by identifying common denominators for the genes based on their individual textual descriptions, annotated functional categories, and predicted protein domains. The orthologous groups in eggNOG contain 1 241 751 genes and provide at least a broad functional description for 77% of them. Users can query the resource for individual genes via a web interface or download the complete set of orthologous groups at http://eggnog.embl.de.

Show MeSH