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How much of the human protein interactome remains to be mapped?

Marc Vidal
2016 Science Signaling  
Mapping the human binary protein-protein interactome illustrates how we could tackle these questions.  ...  Using this empirical framework, we can ask how much of the human binary protein-protein interactome network remains to be mapped.  ...  With the development of additional interaction assays and assuming sufficient funding, a reference map of the human binary protein-protein interactome is within reach by the end of this decade.  ... 
doi:10.1126/scisignal.aaf6030 pmid:27165778 fatcat:vgh3orj6fva63nbyls5ytnbhue

Proteome-Scale Human Interactomics

Katja Luck, Gloria M. Sheynkman, Ivy Zhang, Marc Vidal
2017 TIBS -Trends in Biochemical Sciences. Regular ed  
Keywords network biology; protein-protein interactions; human interactome; binary protein interactions; cocomplex associations; interactome mapping quality; systematic interactome network maps Proteome-scale  ...  towards the generation of a first reference interactome, and reveals new perspectives on the organization of cellular life.  ...  Hill, A. Richardson, and M. Calderwood for helpful discussions, valuable comments and critical reading of the manuscript.  ... 
doi:10.1016/j.tibs.2017.02.006 pmid:28284537 pmcid:PMC5409865 fatcat:4uexon3eeza3tpuvoriezihmyy

A Proteome-Scale Map of the Human Interactome Network

Thomas Rolland, Murat Taşan, Benoit Charloteaux, Samuel J. Pevzner, Quan Zhong, Nidhi Sahni, Song Yi, Irma Lemmens, Celia Fontanillo, Roberto Mosca, Atanas Kamburov, Susan D. Ghiassian (+58 others)
2014 Cell  
Here, we describe a systematic map of ?14,000 high-quality human binary protein-protein interactions. At equal quality, this map is ?  ...  Just as reference genome sequences revolutionized human genetics, reference maps of interactome networks will be critical to fully understand genotype-phenotype relationships.  ...  ACKNOWLEDGMENTS The authors wish to acknowledge past and present members of the Center for Cancer Systems Biology (CCSB) and particularly H. Yu for helpful discussions.  ... 
doi:10.1016/j.cell.2014.10.050 pmid:25416956 pmcid:PMC4266588 fatcat:y52fn56bs5gkjhhe5nxend3dma

Interactome networks

M. Vidal
2008 EJC Supplements  
How far along is the journey towards a complete binary proteineprotein interactome reference map? The answer requires an estimation of the size of such a reference map for any given species.  ...  Similar efforts have been deployed to map the human binary interactome [36,58e62] .  ... 
doi:10.1016/s1359-6349(08)71200-x fatcat:ij56v7qn5fg4beouf5642fcbza

Interactome Networks [chapter]

Anne-Ruxandra Carvunis, Frederick P. Roth, Michael A. Calderwood, Michael E. Cusick, Giulio Superti-Furga, Marc Vidal
2013 Handbook of Systems Biology  
How far along is the journey towards a complete binary proteineprotein interactome reference map? The answer requires an estimation of the size of such a reference map for any given species.  ...  Similar efforts have been deployed to map the human binary interactome [36,58e62] .  ... 
doi:10.1016/b978-0-12-385944-0.00003-4 fatcat:m67aat2kizcyfcdqivox54nv4m

An empirical framework for binary interactome mapping

Kavitha Venkatesan, Jean-François Rual, Alexei Vazquez, Ulrich Stelzl, Irma Lemmens, Tomoko Hirozane-Kishikawa, Tong Hao, Martina Zenkner, Xiaofeng Xin, Kwang-Il Goh, Muhammed A Yildirim, Nicolas Simonis (+28 others)
2008 Nature Methods  
HT-Y2H is suitable to map a significant portion of the human interactome.  ...  We estimate that the human interactome contains B130,000 binary interactions, most of which remain to be mapped.  ...  ACKNOWLEDGMENTS We thank members of CCSB and the Vidal, Barabasi, Wanker and Tavernier laboratories and S. Sahasrabuddhe, R. Bell, R. Chettier and C. Wiggins for helpful discussions; E.  ... 
doi:10.1038/nmeth.1280 pmid:19060904 pmcid:PMC2872561 fatcat:holf7pfp5fhypcvpalpfddvyga

Domain-based prediction of the human isoform interactome provides insights into the functional impact of alternative splicing

Mohamed Ali Ghadie, Luke Lambourne, Marc Vidal, Yu Xia, Andrey Rzhetsky
2017 PLoS Computational Biology  
In the case of human interactome mapping, some studies have used systematic yeast two-hybrid (Y2H) screening to generate large-scale, high-quality maps of the human binary interactome network [13] , whereas  ...  recently culminated in the large-scale mapping of a human isoform interactome [34] .  ... 
doi:10.1371/journal.pcbi.1005717 pmid:28846689 pmcid:PMC5591010 fatcat:wt4whcrn5rhotgni4d5o2rzhgu

Exploring mechanisms of human disease through structurally resolved protein interactome networks

Jishnu Das, Robert Fragoza, Hao Ran Lee, Nicolas A. Cordero, Yu Guo, Michael J. Meyer, Tommy V. Vo, Xiujuan Wang, Haiyuan Yu
2014 Molecular Biosystems  
Within the cell, proteins function by interacting with other proteins as a part of an underlying interactome network.  ...  This network can be determined using interactome mapping -a combination of high-throughput experimental toolkits and curation from small-scale studies.  ...  (F) A high-quality reference human binary interactome comprising B40 000 interactions generated from several large-scale interactome mapping efforts and thousands of small-scale studies.  ... 
doi:10.1039/c3mb70225a pmid:24096645 pmcid:PMC4061614 fatcat:yzowmt35tjhx7boxidwk6o34pm

Mapping, modeling, and characterization of protein–protein interactions on a proteomic scale

TM Cafarelli, A Desbuleux, Y Wang, SG Choi, D De Ridder, M Vidal
2017 Current Opinion in Structural Biology  
A recent systematic binary mapping study assayed pairs of proteins from a space of $13 000 Â 13 000 human open reading frames (ORFs) and identified $14 000 protein-protein interactions (PPIs) among $4300  ...  Binary interaction mapping by yeast two-hybrid (Y2H) Binary mapping by Y2H detects direct physical interactions between two proteins by the reconstitution of a transcription factor that activates reporter  ... 
doi:10.1016/j.sbi.2017.05.003 pmid:28575754 fatcat:ihdjkznrsrhidfd7ilr2h2jhnq

HINT: High-quality protein interactomes and their applications in understanding human disease

Jishnu Das, Haiyuan Yu
2012 BMC Systems Biology  
A global map of protein-protein interactions in cellular systems provides key insights into the workings of an organism.  ...  Results: We develop HINT (http://hint.yulab.org) -a database of high-quality protein-protein interactomes for human, Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Oryza sativa.  ...  Moreover, compared to cocomplex interactome models, binary maps have a greater fraction of transient signaling connections and intercomplex connections [17, 33] .  ... 
doi:10.1186/1752-0509-6-92 pmid:22846459 pmcid:PMC3483187 fatcat:5qgr65otpvaullmpdl55o3tshu

The yeast two-hybrid assay: still finding connections after 25 years

Marc Vidal, Stanley Fields
2014 Nature Methods  
The human protein-protein binary interactome is expected to contain on the order of a few hundred-thousand interactions.  ...  The current status of the field suggests the possibility that a reference human interactome map may become available by the end of this decade.  ...  COMPETING FINANCIAL INTERESTS The authors declare no competing financial interests.  ... 
doi:10.1038/nmeth.3182 pmid:25584376 fatcat:ppxpfqixdnbalm7b63ywachx4a

High-Quality Binary Protein Interaction Map of the Yeast Interactome Network

H. Yu, P. Braun, M. A. Yildirim, I. Lemmens, K. Venkatesan, J. Sahalie, T. Hirozane-Kishikawa, F. Gebreab, N. Li, N. Simonis, T. Hao, J.-F. Rual (+22 others)
2008 Science  
, and CCSB-YI1; Fig. 3C ), as well as in new versions of our C. elegans and human interactome maps ( fig.  ...  Because a large fraction of the yeast binary interactome remains to be mapped, we developed an empirically controlled mapping framework to produce a "second-generation" high-quality, high-throughput Y2H  ... 
doi:10.1126/science.1158684 pmid:18719252 pmcid:PMC2746753 fatcat:goibtsf3yraz7na5nmylvdzaaa

A Physical Map of the 1-Gigabase Bread Wheat Chromosome 3B

E. Paux, P. Sourdille, J. Salse, C. Saintenac, F. Choulet, P. Leroy, A. Korol, M. Michalak, S. Kianian, W. Spielmeyer, E. Lagudah, D. Somers (+11 others)
2008 Science  
, and CCSB-YI1; Fig. 3C ), as well as in new versions of our C. elegans and human interactome maps ( fig.  ...  Because a large fraction of the yeast binary interactome remains to be mapped, we developed an empirically controlled mapping framework to produce a "second-generation" high-quality, high-throughput Y2H  ... 
doi:10.1126/science.1161847 pmid:18832645 fatcat:pao6ziq3evbgrntv4jgdikqk5y

E. coli network upgrade

Ulrich Stelzl
2014 Nature Biotechnology  
a high-resolution E. coli interactome map-the most detailed map of its kind for any organism.  ...  Rajagopala et al. 1 Yeast two-hybrid binary network Figure 1 The path toward a detailed, highresolution E. coli interactome map starts by combining binary protein-protein interaction data from yeast  ...  COMPETING FINANCIAL INTERESTS The authors declare no competing financial interests. COMPETING FINANCIAL INTERESTS The author declares no competing financial interests.  ... 
doi:10.1038/nbt.2848 pmid:24727776 fatcat:zt5cpmnrkba37ozbutwvd6iomq

Edgotype: a fundamental link between genotype and phenotype

Nidhi Sahni, Song Yi, Quan Zhong, Noor Jailkhani, Benoit Charloteaux, Michael E Cusick, Marc Vidal
2013 Current Opinion in Genetics and Development  
Accordingly, mechanistic understanding of human disease will require understanding of how disease-causing mutations affect systems or interactome properties.  ...  Classical 'one-gene/one-disease' models cannot fully reconcile with the increasingly appreciated prevalence of complicated genotype-to-phenotype associations in human disease.  ...  A new generation of binary interactome mapping is underway with enhanced network completeness and resolution.  ... 
doi:10.1016/j.gde.2013.11.002 pmid:24287335 pmcid:PMC3902775 fatcat:txoynrwgqvhb7ciuszpajmo5nu
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