Meta-Analysis

. 2022 Jul 5;50(W1):W623-W632.

doi: 10.1093/nar/gkac330.

The Quest for Orthologs orthology benchmark service in 2022

Yannis Nevers^{1

2}, Tamsin E M Jones³, Dushyanth Jyothi⁴, Bethan Yates³, Meritxell Ferret⁵, Laura Portell-Silva⁵, Laia Codo⁵, Salvatore Cosentino⁶, Marina Marcet-Houben^{5

7}, Anna Vlasova^{5

7}, Laetitia Poidevin^{8

9}, Arnaud Kress^{8

9}, Mark Hickman¹⁰, Emma Persson¹¹, Ivana Piližota¹², Cristina Guijarro-Clarke¹²; OpenEBench team the Quest for Orthologs Consortium; Wataru Iwasaki^{6

13}, Odile Lecompte⁸, Erik Sonnhammer¹¹, David S Roos¹⁰, Toni Gabaldón^{5

7

14

15}, David Thybert¹², Paul D Thomas¹⁶, Yanhui Hu¹⁷, David M Emms¹⁸, Elspeth Bruford^{3

19}, Salvador Capella-Gutierrez⁵, Maria J Martin⁴, Christophe Dessimoz^{1

2

20

21}, Adrian Altenhoff^{2

22}

Collaborators, Affiliations

Collaborators

OpenEBench team the Quest for Orthologs Consortium:
Adrian Altenhoff, Elspeth A Bruford, Salvatore Cosentino, Christophe Dessimoz, Ingo Ebersberger, David M Emms, Toni Gabaldón, Natasha Glover, Cristina Guijarro-Clarke, Mark Hickman, Yanhui Hu, Wataru Iwasaki, Tamsin E M Jones, Dushyanth Jyothi, Arnaud Kress, Odile Lecompte, Benjamin Linard, Marina Marcet-Houben, Maria J Martin, Yannis Nevers, Emma Persson, Ivana Piližota, Laetitia Poidevin, David S Roos, Erik Sonhammer, Paul D Thomas, David Thybert, Klaas Vandepoele, Anna Vlasova, Bethan Yates, Salvador Capella-Gutierrez, Laia Codó, Meritxell Ferret, Asier Gonzalez-Uriarte, Javier Garrayo-Ventas, Laura Portell-Silva, Dmitry Repchevsky, Vicky Sundesha

Affiliations

¹ Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
² Swiss Institute for Bioinformatics, University of Lausanne, Lausanne, Switzerland.
³ HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
⁴ Protein Function development, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
⁵ Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, 1-3 08034 Barcelona, Spain.
⁶ Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan.
⁷ Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
⁸ Department of Computer Science, ICube, UMR 7357, Centre de Recherche en Biomédecine de Strasbourg, University of Strasbourg, CNRS, Strasbourg, France.
⁹ BiGEst-ICube Platform, ICube, UMR 7357, Centre de Recherche en Biomédecine de Strasbourg, University of Strasbourg, CNRS, Strasbourg, France.
¹⁰ Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
¹¹ Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
¹² European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
¹³ Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Japan.
¹⁴ Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
¹⁵ Centro de Investigaciones Biomédicas en Red de Enfermedades Infecciosas, Barcelona, Spain.
¹⁶ Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA.
¹⁷ Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA.
¹⁸ Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK.
¹⁹ Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.
²⁰ Department of Computer Science, University College London, London, UK.
²¹ Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
²² Computer Science Department, ETH Zurich, Zurich, Switzerland.

PMID: 35552456
PMCID: PMC9252809
DOI: 10.1093/nar/gkac330

Meta-Analysis

The Quest for Orthologs orthology benchmark service in 2022

Yannis Nevers et al. Nucleic Acids Res. 2022.

. 2022 Jul 5;50(W1):W623-W632.

doi: 10.1093/nar/gkac330.

Authors

Collaborators

OpenEBench team the Quest for Orthologs Consortium:
Adrian Altenhoff, Elspeth A Bruford, Salvatore Cosentino, Christophe Dessimoz, Ingo Ebersberger, David M Emms, Toni Gabaldón, Natasha Glover, Cristina Guijarro-Clarke, Mark Hickman, Yanhui Hu, Wataru Iwasaki, Tamsin E M Jones, Dushyanth Jyothi, Arnaud Kress, Odile Lecompte, Benjamin Linard, Marina Marcet-Houben, Maria J Martin, Yannis Nevers, Emma Persson, Ivana Piližota, Laetitia Poidevin, David S Roos, Erik Sonhammer, Paul D Thomas, David Thybert, Klaas Vandepoele, Anna Vlasova, Bethan Yates, Salvador Capella-Gutierrez, Laia Codó, Meritxell Ferret, Asier Gonzalez-Uriarte, Javier Garrayo-Ventas, Laura Portell-Silva, Dmitry Repchevsky, Vicky Sundesha

Affiliations

¹ Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
² Swiss Institute for Bioinformatics, University of Lausanne, Lausanne, Switzerland.
³ HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
⁴ Protein Function development, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
⁵ Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, 1-3 08034 Barcelona, Spain.
⁶ Department of Biological Sciences, Graduate School of Science, the University of Tokyo, Tokyo, Japan.
⁷ Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain.
⁸ Department of Computer Science, ICube, UMR 7357, Centre de Recherche en Biomédecine de Strasbourg, University of Strasbourg, CNRS, Strasbourg, France.
⁹ BiGEst-ICube Platform, ICube, UMR 7357, Centre de Recherche en Biomédecine de Strasbourg, University of Strasbourg, CNRS, Strasbourg, France.
¹⁰ Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
¹¹ Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.
¹² European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK.
¹³ Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Japan.
¹⁴ Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
¹⁵ Centro de Investigaciones Biomédicas en Red de Enfermedades Infecciosas, Barcelona, Spain.
¹⁶ Department of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90032, USA.
¹⁷ Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA.
¹⁸ Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK.
¹⁹ Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.
²⁰ Department of Computer Science, University College London, London, UK.
²¹ Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
²² Computer Science Department, ETH Zurich, Zurich, Switzerland.

PMID: 35552456
PMCID: PMC9252809
DOI: 10.1093/nar/gkac330

Abstract

The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existing and new methods of orthology inference (the bedrock for many comparative genomics and phylogenetic analysis) over a standard dataset and through common procedures. The Quest for Orthologs Consortium is dedicated to maintaining the resource up to date, through regular updates of the Reference Proteomes and increasingly accessible data through the OpenEBench platform. For this update, we have added a new benchmark based on curated orthology assertion from the Vertebrate Gene Nomenclature Committee, and provided an example meta-analysis of the public predictions present on the platform.

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Figures

**Graphical Abstract**
The Quest for Orthologs benchmarking service helps orthology inference methods developers compare their methods on standardized benchmarks, users to choose appropriate methods and provides data for consensus orthology calls.

**Figure 1.**
VGNC symbol Benchmark. Results of each method with True Positive Rate (x-axis) as a recall measure and Positive Predictive Value (y-axis) as a precision measure. Note: The axes have been truncated to maximize the spread of the methods on the figure. As a result, the y-axis shows a significantly larger variation in values than the x-axis

**Figure 2.**
Orthologous pairs inferred by individual methods. Number of pairs inferred by public methods included in the benchmarking platform. Subsections of the bars represent the number of methods that share the same pairs. Methods are ranked by the number of pairs they share with other methods (non-green part of the stacked bars).

**Figure 3.**
Pairwise comparisons between predictions of public methods. The heatmap shows the proportion of the pairs inferred by methods on the right side that are recapitulated by methods on the bottom. The heatmap is hierarchically clustered on rows and columns by similarity with the corresponding trees shown.

See this image and copyright information in PMC

References

1. Fitch W.M. Distinguishing homologous from analogous proteins. Syst. Zool. 1970; 19:99–113. - PubMed
1. Nevers Y., Defosset A., Lecompte O.. Pontarotti P. Orthology: promises and challenges. Evolutionary Biology—A Transdisciplinary Approach. 2020; Cham: Springer International Publishing; 203–228.
1. Altenhoff A.M., Glover N.M., Dessimoz C.. Inferring orthology and paralogy. Methods Mol. Biol. 2019; 1910:149–175. - PubMed
1. Glover N., Dessimoz C., Ebersberger I., Forslund S.K., Gabaldón T., Huerta-Cepas J., Martin M.-J., Muffato M., Patricio M., Pereira C.et al. .. Advances and applications in the quest for orthologs. Mol. Biol. Evol. 2019; 36:2157–2164. - PMC - PubMed
1. Forslund K., Pereira C., Capella-Gutierrez S., da Silva A.S., Altenhoff A., Huerta-Cepas J., Muffato M., Patricio M., Vandepoele K., Ebersberger I.et al. .. Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinformatics. 2018; 34:323–329. - PMC - PubMed

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The Quest for Orthologs orthology benchmark service in 2022

Collaborators

Affiliations

The Quest for Orthologs orthology benchmark service in 2022

Authors

Collaborators

Affiliations

Abstract

Figures

References

Publication types

MeSH terms

Substances

Grants and funding

LinkOut - more resources

Full Text Sources