ArticleMolecular systems biology2016
An inter-species protein-protein interaction network across vast evolutionary distance.
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Article in Molecular systems biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21citing papers in PubMed
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21 citing papers in PubMed.
- Condensates and cell states: A new paradigm for understanding tumor biology.Biophysical journal · 2026Review
- Recurrent innovation of protein-protein interactions in the Drosophila piRNA pathway.The EMBO journal · 2026Article
- Cheminformatic analysis of protein surfaces provides binding site insights and informs identification strategies.Future medicinal chemistry · 2025Article
- Pooled PPIseq: Screening the SARS-CoV-2 and human interface with a scalable multiplexed protein-protein interaction assay platform.PloS one · 2025Article
- Review
- A Genomics Resource for 12 Edible Seaweeds to Predict Seaweed-Secreted Peptides with Potential Anti-Cancer Function.Biology · 2022Article
- A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19.Research square · 2022Article
- Humanized yeast to model human biology, disease and evolution.Disease models & mechanisms · 2022Review
- Comparative Network Biology Discovers Protein Complexes That Underline Cellular Differentiation in Anabaena sp.Molecular & cellular proteomics : MCP · 2022Article
- Are transient protein-protein interactions more dispensable?PLoS computational biology · 2022Article
- Frequent Assembly of Chimeric Complexes in the Protein Interaction Network of an Interspecies Yeast Hybrid.Molecular biology and evolution · 2021Article
- Protein Complexes Form a Basis for Complex Hybrid Incompatibility.Frontiers in genetics · 2021Review
- Mutation Edgotype Drives Fitness Effect in Human.Frontiers in bioinformatics · 2021Article
- A Genetic Screen for Human Genes Suppressing FUS Induced Toxicity in Yeast.G3 (Bethesda, Md.) · 2020Article
- Estimating dispensable content in the human interactome.Nature communications · 2019Article
- Evolutionary divergence of the nuclear pore complex from fungi to metazoans.Protein science : a publication of the Protein Society · 2019Article
- Network enhancement as a general method to denoise weighted biological networks.Nature communications · 2018Article
- INTERSPIA: a web application for exploring the dynamics of protein-protein interactions among multiple species.Nucleic acids research · 2018Article
- Proteome-Scale Human Interactomics.Trends in biochemical sciences · 2017Review
- Bacterial protein meta-interactomes predict cross-species interactions and protein function.BMC bioinformatics · 2017Article
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Authors and funding
31 authors.
Quan ZhongCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA Department of Biological Sciences, Wright State University, Dayton, OH, USA marc_vidal@dfci.harvard.edu fritz.roth@utoronto.ca brandon.xia@mcgill.ca quan.zhong@wright.edu.
Samuel J PevznerCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA Department of Biomedical Engineering, Boston University, Boston, MA, USA Boston University School of Medicine, Boston, MA, USA.
Tong HaoCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Yang WangCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Roberto MoscaJoint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona Catalonia, Spain.
Jörg MencheCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Center for Complex Network Research (CCNR) and Department of Physics, Northeastern University, Boston, MA, USA.ORCID http://orcid.org/0000-0002-1583-6404
Mikko TaipaleWhitehead Institute for Biomedical Research, Cambridge, MA, USA.
Murat TaşanCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON, Canada Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada.
Changyu FanCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Xinping YangCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Patrick HaleyCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Ryan R MurrayCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Flora MerCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Fana GebreabCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Stanley TamCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Andrew MacWilliamsCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Amélie DricotCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Patrick ReichertCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Balaji SanthanamCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Lila GhamsariCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Michael A CalderwoodCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-6475-1418
Thomas RollandCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Benoit CharloteauxCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Susan LindquistWhitehead Institute for Biomedical Research, Cambridge, MA, USA Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
Albert-László BarabásiCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Center for Complex Network Research (CCNR) and Department of Physics, Northeastern University, Boston, MA, USA Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
David E HillCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0001-5192-0921
Patrick AloyJoint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona Catalonia, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
Michael E CusickCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA.
Yu XiaCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Bioengineering, McGill University, Montreal, QC, Canada marc_vidal@dfci.harvard.edu fritz.roth@utoronto.ca brandon.xia@mcgill.ca quan.zhong@wright.edu.
Frederick P RothCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Departments of Molecular Genetics and Computer Science, University of Toronto, Toronto, ON, Canada Donnelly Centre, University of Toronto, Toronto, ON, Canada Lunenfeld-Tanenbaum Research Institute, Mt. Sinai Hospital, Toronto, ON, Canada Canadian Institute for Advanced Research, Toronto, ON, Canada marc_vidal@dfci.harvard.edu fritz.roth@utoronto.ca brandon.xia@mcgill.ca quan.zhong@wright.edu.
Marc VidalCenter for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA Department of Genetics, Harvard Medical School, Boston, MA, USA marc_vidal@dfci.harvard.edu fritz.roth@utoronto.ca brandon.xia@mcgill.ca quan.zhong@wright.edu.ORCID http://orcid.org/0000-0003-3391-5410
Funding
The C. elegans Interactome ProjectR01HG001715 · NHGRI · MASSACHUSETTS GENERAL HOSPITAL · PI HILL, DAVID E., ROTH, FREDERICK P · 1998 to 2010
$16.5MMapping the first half of the REFERENCE human binary protein interactomeU01HG001715 · NHGRI · DANA-FARBER CANCER INST · PI HILL, DAVID E., ROTH, FREDERICK P · 2012 to 2014
$5.4MResource ProjectU41HG001715 · NHGRI · DANA-FARBER CANCER INST · PI HILL, DAVID E. · 2015 to 2017
$4.7MA S. cerevisiae high-coverage high-quality protein-protein binary interactome mapR01HG006061 · NHGRI · DANA-FARBER CANCER INST · PI CALDERWOOD, MICHAEL A, HILL, DAVID E. · 2011 to 2014
$3.1MIntramural NIH HHSNHGRI NIH HHS R01 HG001715NHGRI NIH HHS R01-HG001715NHGRI NIH HHS R01 HG006061NHGRI NIH HHS R01-HG006061NHGRI NIH HHS U01 HG001715NHGRI NIH HHS U41 HG001715
Abstract
In cellular systems, biophysical interactions between macromolecules underlie a complex web of functional interactions. How biophysical and functional networks are coordinated, whether all biophysical interactions correspond to functional interactions, and how such biophysical-versus-functional network coordination is shaped by evolutionary forces are all largely unanswered questions. Here, we investigate these questions using an "inter-interactome" approach. We systematically probed the yeast and human proteomes for interactions between proteins from these two species and functionally characterized the resulting inter-interactome network. After a billion years of evolutionary divergence, the yeast and human proteomes are still capable of forming a biophysical network with properties that resemble those of intra-species networks. Although substantially reduced relative to intra-species networks, the levels of functional overlap in the yeast-human inter-interactome network uncover significant remnants of co-functionality widely preserved in the two proteomes beyond human-yeast homologs. Our data support evolutionary selection against biophysical interactions between proteins with little or no co-functionality. Such non-functional interactions, however, represent a reservoir from which nascent functional interactions may arise.
Indexed as
Computational BiologyDatabases, ProteinEvolution, MolecularFungal ProteinsHumansProtein Interaction MappingProteomeFungal ProteinsProteomeCross‐species complementationNetwork evolutionSelection
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