Network-based prediction of protein interactions.
István Kovács,Katja Luck,Kerstin Spirohn,Yang Wang,Carl Pollis,Sadie Schlabach,Wenting Bian,Dae-Kyum Kim,Dae-Kyum Kim,Nishka Kishore,Nishka Kishore,Tong Hao,Michael A. Calderwood,Marc Vidal,Albert-László Barabási +14 more
Reads0
Chats0
TLDR
It is shown that proteins tend to interact if one is similar to the other’s partners and that PPI prediction based on this principle is highly accurate and can offer mechanistic insights into disease mechanisms and complement future experimental efforts to complete the human interactome.Abstract:
Despite exceptional experimental efforts to map out the human interactome, the continued data incompleteness limits our ability to understand the molecular roots of human disease. Computational tools offer a promising alternative, helping identify biologically significant, yet unmapped protein-protein interactions (PPIs). While link prediction methods connect proteins on the basis of biological or network-based similarity, interacting proteins are not necessarily similar and similar proteins do not necessarily interact. Here, we offer structural and evolutionary evidence that proteins interact not if they are similar to each other, but if one of them is similar to the other's partners. This approach, that mathematically relies on network paths of length three (L3), significantly outperforms all existing link prediction methods. Given its high accuracy, we show that L3 can offer mechanistic insights into disease mechanisms and can complement future experimental efforts to complete the human interactome.read more
Citations
More filters
Journal ArticleDOI
A reference map of the human binary protein interactome
Katja Luck,Dae-Kyum Kim,Luke Lambourne,Kerstin Spirohn,Bridget E. Begg,Wenting Bian,Ruth Brignall,Tiziana M. Cafarelli,Francisco J. Campos-Laborie,Benoit Charloteaux,Dong-Sic Choi,Atina G. Cote,Meaghan Daley,Steven Deimling,Alice Desbuleux,Amélie Dricot,Marinella Gebbia,Madeleine F. Hardy,Nishka Kishore,Jennifer J. Knapp,István Kovács,István Kovács,Irma Lemmens,Irma Lemmens,Miles W. Mee,Joseph C. Mellor,Carl Pollis,Carles Pons,Aaron Richardson,Sadie Schlabach,Bridget Teeking,Anupama Yadav,Mariana Babor,Dawit Balcha,Omer Basha,Christian Bowman-Colin,Suet-Feung Chin,Soon Gang Choi,Claudia Colabella,Georges Coppin,Cassandra D’Amata,David De Ridder,Steffi De Rouck,Steffi De Rouck,Miquel Duran-Frigola,Hanane Ennajdaoui,Florian Goebels,Liana Goehring,Anjali Gopal,Ghazal Haddad,Elodie Hatchi,Mohamed Helmy,Yves Jacob,Yves Jacob,Yoseph Kassa,Serena Landini,Roujia Li,Natascha van Lieshout,Andrew MacWilliams,Dylan Markey,Joseph N. Paulson,Joseph N. Paulson,Sudharshan Rangarajan,John Rasla,Ashyad Rayhan,Thomas Rolland,Adriana San-Miguel,Yun Shen,Dayag Sheykhkarimli,Gloria M. Sheynkman,Eyal Simonovsky,Murat Tasan,Alexander O. Tejeda,Vincent Tropepe,Jean-Claude Twizere,Yang Wang,Robert J. Weatheritt,Jochen Weile,Yu Xia,Yu Xia,Xinping Yang,Esti Yeger-Lotem,Quan Zhong,Patrick Aloy,Gary D. Bader,Javier De Las Rivas,Suzanne Gaudet,Tong Hao,Janusz Rak,Jan Tavernier,Jan Tavernier,David E. Hill,Marc Vidal,Frederick P. Roth,Michael A. Calderwood +94 more
TL;DR: The utility of HuRI is demonstrated in identifying the specific subcellular roles of protein–protein interactions and in identifying potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases.
Journal ArticleDOI
Network-based prediction of drug combinations.
TL;DR: A network-based methodology to identify efficacious drug combinations for specific diseases is proposed, and it is found that successful combinations tend to target separate neighbourhoods of the disease module in the human interactome.
Journal ArticleDOI
Link prediction techniques, applications, and performance: A survey
TL;DR: Learning-based methods are covered in addition to clustering-based and information-theoretic models in a separate group, and the experimental results of similarity and some other representative approaches are tabulated and discussed.
Journal ArticleDOI
Molecular networks in Network Medicine: Development and applications.
Edwin K. Silverman,Harald H.H.W. Schmidt,Eleni Anastasiadou,Lucia Altucci,Marco Angelini,Lina Badimon,Jean-Luc Balligand,Giuditta Benincasa,Giovambattista Capasso,Federica Conte,Antonella Di Costanzo,Lorenzo Farina,Giulia Fiscon,Laurent Gatto,Michele Gentili,Joseph Loscalzo,Cinzia Marchese,Claudio Napoli,Paola Paci,Manuela Petti,John Quackenbush,John Quackenbush,Paolo Tieri,Davide Viggiano,Gemma Vilahur,Kimberly Glass,Kimberly Glass,Jan Baumbach,Jan Baumbach +28 more
TL;DR: This work discusses briefly the types of molecular data that are used in molecular network analyses, survey the analytical methods for inferring molecular networks, and review efforts to validate and visualize molecular networks.
Journal ArticleDOI
Computational network biology: Data, models, and applications
Chuang Liu,Yifang Ma,Jing Zhao,Ruth Nussinov,Ruth Nussinov,Yi-Cheng Zhang,Yi-Cheng Zhang,Feixiong Cheng,Feixiong Cheng,Feixiong Cheng,Zi-Ke Zhang,Zi-Ke Zhang +11 more
TL;DR: This review summarizes the recent developments of computational network biology, first introducing various types of biological networks and network structural properties, and then reviewing the network-based approaches, ranging from some network metrics to the complicated machine-learning methods.
References
More filters
Journal ArticleDOI
The Strength of Weak Ties
TL;DR: In this paper, it is argued that the degree of overlap of two individuals' friendship networks varies directly with the strength of their tie to one another, and the impact of this principle on diffusion of influence and information, mobility opportunity, and community organization is explored.
Journal ArticleDOI
STRING v10: protein–protein interaction networks, integrated over the tree of life
Damian Szklarczyk,Andrea Franceschini,Stefan Wyder,Kristoffer Forslund,Davide Heller,Jaime Huerta-Cepas,Milan Simonovic,Alexander Roth,Alberto Santos,Kalliopi Tsafou,Michael Kuhn,Peer Bork,Lars Juhl Jensen,Christian von Mering +13 more
TL;DR: H hierarchical and self-consistent orthology annotations are introduced for all interacting proteins, grouping the proteins into families at various levels of phylogenetic resolution in the STRING database.
Journal ArticleDOI
A comprehensive analysis of protein–protein interactions in Saccharomyces cerevisiae
Peter Uetz,Loic Giot,Gerard Cagney,Traci A. Mansfield,Richard S. Judson,James R. Knight,Daniel Lockshon,Vaibhav A. Narayan,Maithreyan Srinivasan,Pascale Pochart,Alia Qureshi-Emili,Ying Li,Brian C. Godwin,Diana Conover,Theodore S. Kalbfleisch,Govindan Vijayadamodar,Meijia Yang,Mark Johnston,Stanley Fields,Jonathan M. Rothberg +19 more
TL;DR: Examination of large-scale yeast two-hybrid screens reveals interactions that place functionally unclassified proteins in a biological context, interactions between proteins involved in the same biological function, and interactions that link biological functions together into larger cellular processes.
Journal IssueDOI
The link-prediction problem for social networks
David Liben-Nowell,Jon Kleinberg +1 more
TL;DR: Experiments on large coauthorship networks suggest that information about future interactions can be extracted from network topology alone, and that fairly subtle measures for detecting node proximity can outperform more direct measures.
Journal ArticleDOI
Network Medicine: A Network-Based Approach to Human Disease
TL;DR: Advances in this direction are essential for identifying new disease genes, for uncovering the biological significance of disease-associated mutations identified by genome-wide association studies and full-genome sequencing, and for identifying drug targets and biomarkers for complex diseases.