Literature DB >> 28284537

Proteome-Scale Human Interactomics.

Katja Luck1, Gloria M Sheynkman2, Ivy Zhang3, Marc Vidal4.   

Abstract

Cellular functions are mediated by complex interactome networks of physical, biochemical, and functional interactions between DNA sequences, RNA molecules, proteins, lipids, and small metabolites. A thorough understanding of cellular organization requires accurate and relatively complete models of interactome networks at proteome scale. The recent publication of four human protein-protein interaction (PPI) maps represents a technological breakthrough and an unprecedented resource for the scientific community, heralding a new era of proteome-scale human interactomics. Our knowledge gained from these and complementary studies provides fresh insights into the opportunities and challenges when analyzing systematically generated interactome data, defines a clear roadmap towards the generation of a first reference interactome, and reveals new perspectives on the organization of cellular life.
Copyright © 2017 Elsevier Ltd. All rights reserved.

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Year:  2017        PMID: 28284537      PMCID: PMC5409865          DOI: 10.1016/j.tibs.2017.02.006

Source DB:  PubMed          Journal:  Trends Biochem Sci        ISSN: 0968-0004            Impact factor:   13.807


  65 in total

1.  A human interactome in three quantitative dimensions organized by stoichiometries and abundances.

Authors:  Marco Y Hein; Nina C Hubner; Ina Poser; Jürgen Cox; Nagarjuna Nagaraj; Yusuke Toyoda; Igor A Gak; Ina Weisswange; Jörg Mansfeld; Frank Buchholz; Anthony A Hyman; Matthias Mann
Journal:  Cell       Date:  2015-10-22       Impact factor: 41.582

2.  Estimating and improving protein interaction error rates.

Authors:  Patrik D'haeseleer; George M Church
Journal:  Proc IEEE Comput Syst Bioinform Conf       Date:  2004

3.  How perfect can protein interactomes be?

Authors:  Emmanuel D Levy; Christian R Landry; Stephen W Michnick
Journal:  Sci Signal       Date:  2009-03-03       Impact factor: 8.192

Review 4.  A million peptide motifs for the molecular biologist.

Authors:  Peter Tompa; Norman E Davey; Toby J Gibson; M Madan Babu
Journal:  Mol Cell       Date:  2014-07-17       Impact factor: 17.970

Review 5.  A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics.

Authors:  Alexey I Nesvizhskii
Journal:  J Proteomics       Date:  2010-09-08       Impact factor: 4.044

6.  How complete are current yeast and human protein-interaction networks?

Authors:  G Traver Hart; Arun K Ramani; Edward M Marcotte
Journal:  Genome Biol       Date:  2006       Impact factor: 13.583

7.  Phospho-tyrosine dependent protein-protein interaction network.

Authors:  Arndt Grossmann; Nouhad Benlasfer; Petra Birth; Anna Hegele; Franziska Wachsmuth; Luise Apelt; Ulrich Stelzl
Journal:  Mol Syst Biol       Date:  2015-03-26       Impact factor: 11.429

8.  An inter-species protein-protein interaction network across vast evolutionary distance.

Authors:  Quan Zhong; Samuel J Pevzner; Tong Hao; Yang Wang; Roberto Mosca; Jörg Menche; Mikko Taipale; Murat Taşan; Changyu Fan; Xinping Yang; Patrick Haley; Ryan R Murray; Flora Mer; Fana Gebreab; Stanley Tam; Andrew MacWilliams; Amélie Dricot; Patrick Reichert; Balaji Santhanam; Lila Ghamsari; Michael A Calderwood; Thomas Rolland; Benoit Charloteaux; Susan Lindquist; Albert-László Barabási; David E Hill; Patrick Aloy; Michael E Cusick; Yu Xia; Frederick P Roth; Marc Vidal
Journal:  Mol Syst Biol       Date:  2016-04-22       Impact factor: 11.429

9.  Literature-curated protein interaction datasets.

Authors:  Michael E Cusick; Haiyuan Yu; Alex Smolyar; Kavitha Venkatesan; Anne-Ruxandra Carvunis; Nicolas Simonis; Jean-François Rual; Heather Borick; Pascal Braun; Matija Dreze; Jean Vandenhaute; Mary Galli; Junshi Yazaki; David E Hill; Joseph R Ecker; Frederick P Roth; Marc Vidal
Journal:  Nat Methods       Date:  2009-01       Impact factor: 28.547

10.  A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.

Authors:  Tommy V Vo; Jishnu Das; Michael J Meyer; Nicolas A Cordero; Nurten Akturk; Xiaomu Wei; Benjamin J Fair; Andrew G Degatano; Robert Fragoza; Lisa G Liu; Akihisa Matsuyama; Michelle Trickey; Sachi Horibata; Andrew Grimson; Hiroyuki Yamano; Minoru Yoshida; Frederick P Roth; Jeffrey A Pleiss; Yu Xia; Haiyuan Yu
Journal:  Cell       Date:  2016-01-14       Impact factor: 41.582

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  47 in total

Review 1.  Pathway perturbations in signaling networks: Linking genotype to phenotype.

Authors:  Yongsheng Li; Daniel J McGrail; Natasha Latysheva; Song Yi; M Madan Babu; Nidhi Sahni
Journal:  Semin Cell Dev Biol       Date:  2018-05-10       Impact factor: 7.727

2.  Protein Interactomics by Two-Hybrid Methods.

Authors:  Soon Gang Choi; Aaron Richardson; Luke Lambourne; David E Hill; Marc Vidal
Journal:  Methods Mol Biol       Date:  2018

3.  A Cross-Linking-Aided Immunoprecipitation/Mass Spectrometry Workflow Reveals Extensive Intracellular Trafficking in Time-Resolved, Signal-Dependent Epidermal Growth Factor Receptor Proteome.

Authors:  Yue Chen; Mei Leng; Yankun Gao; Dongdong Zhan; Jong Min Choi; Lei Song; Kai Li; Xia Xia; Chunchao Zhang; Mingwei Liu; Shuhui Ji; Antrix Jain; Alexander B Saltzman; Anna Malovannaya; Jun Qin; Sung Yun Jung; Yi Wang
Journal:  J Proteome Res       Date:  2019-09-09       Impact factor: 4.466

4.  Network Analysis of UBE3A/E6AP-Associated Proteins Provides Connections to Several Distinct Cellular Processes.

Authors:  Gustavo Martínez-Noël; Katja Luck; Simone Kühnle; Alice Desbuleux; Patricia Szajner; Jeffrey T Galligan; Diana Rodriguez; Leon Zheng; Kathleen Boyland; Flavian Leclere; Quan Zhong; David E Hill; Marc Vidal; Peter M Howley
Journal:  J Mol Biol       Date:  2018-02-06       Impact factor: 5.469

Review 5.  Molecular networks in Network Medicine: Development and applications.

Authors:  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; Paolo Tieri; Davide Viggiano; Gemma Vilahur; Kimberly Glass; Jan Baumbach
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2020-04-19

6.  High-Dimensional Bayesian Network Inference From Systems Genetics Data Using Genetic Node Ordering.

Authors:  Lingfei Wang; Pieter Audenaert; Tom Michoel
Journal:  Front Genet       Date:  2019-12-20       Impact factor: 4.599

Review 7.  Mapping the protein-protein and genetic interactions of cancer to guide precision medicine.

Authors:  Mehdi Bouhaddou; Manon Eckhardt; Zun Zar Chi Naing; Minkyu Kim; Trey Ideker; Nevan J Krogan
Journal:  Curr Opin Genet Dev       Date:  2019-07-06       Impact factor: 5.578

Review 8.  Gain-of-Function Mutations: An Emerging Advantage for Cancer Biology.

Authors:  Yongsheng Li; Yunpeng Zhang; Xia Li; Song Yi; Juan Xu
Journal:  Trends Biochem Sci       Date:  2019-04-29       Impact factor: 13.807

Review 9.  Precision medicine - networks to the rescue.

Authors:  Anupama Yadav; Marc Vidal; Katja Luck
Journal:  Curr Opin Biotechnol       Date:  2020-03-18       Impact factor: 9.740

10.  Correcting the F508del-CFTR variant by modulating eukaryotic translation initiation factor 3-mediated translation initiation.

Authors:  Darren M Hutt; Salvatore Loguercio; Daniela Martino Roth; Andrew I Su; William E Balch
Journal:  J Biol Chem       Date:  2018-07-13       Impact factor: 5.157

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