eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

By Sean Powell, Damian Szklarczyk, Kalliopi Trachana, Alexander C. J. Roth, Michael Kuhn, Jean Muller, Roland Arnold, Thomas Rattei, Ivica Letunic, Tobias Doerks and 3 more. Nucleic Acids Res., 2011

537 citations recorded by the source corpus.

Orthologous relationships form the basis of most comparative genomic and metagenomic studies and are essential for proper phylogenetic and functional analyses. The third version of the eggNOG database (http://eggnog.embl.de) contains non-supervised orthologous groups constructed from 1133 organisms, doubling the number of genes with orthology assignment compared to eggNOG v2. The new release is the result of a number of improvements and expansions: (i) the underlying homology searches are now based on the SIMAP database; (ii) the orthologous groups have been extended to 41 levels of selected taxonomic ranges enabling much more fine-grained orthology assignments; and (iii) the newly designed web page is considerably faster with more functionality. In total, eggNOG v3 contains 721 801 orthologous groups, encompassing a total of 4 396 591 genes. Additionally, we updated 4873 and 4850 original COGs and KOGs, respectively, to include all 1133 organisms. At the universal level, covering all three domains of life, 101 208 orthologous groups are available, while the others are applicable at 40 more limited taxonomic ranges. Each group is amended by multiple sequence alignments and maximum-likelihood trees and broad functional descriptions are provided for 450 904 orthologous groups (62.5%).

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b640e86d2f1390f4c31c32a6beb5ad5164d219b8

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Citations in the corpus

Structure and function of the global ocean microbiome (2015, methodology): “Thus, we first mapped the OM-RGC to known gene families, represented by clusters of orthologous groups [OGs, (46)] and selected prokaryotic genes to ensure comparability between the data sets.”
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data (2016, methodology): “MEGAN CE offers a new eggNOG viewer that is based on a classification of orthologous groups in which reads are binned to “ clusters of orthologous groups ” (COGs) and “ non-supervised orthologous groups ” that appear as leaves of the eggNOG classification [15].”
STRING v9.1: protein-protein interaction networks, with increased coverage and integration (2012, methodology): “In particular, we will describe how STRING increasingly makes use of externally provided orthology information [from the eggNOG database (33)] to better integrate evidence across distinct organisms.”
Protein Complexes in Bacteria (2015, methodology): “proteins were mapped to each other using common COGs, NOGs, or bactNOGs [10]”
OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs (2012, background): “(7,8) have embraced this concept and now provide orthology classifications at several major radiations across the tree of life.”