Literature DB >> 27708008

A global genetic interaction network maps a wiring diagram of cellular function.

Michael Costanzo1, Benjamin VanderSluis2, Elizabeth N Koch3, Anastasia Baryshnikova4, Carles Pons3, Guihong Tan1, Wen Wang3, Matej Usaj1, Julia Hanchard5, Susan D Lee6, Vicent Pelechano7, Erin B Styles5, Maximilian Billmann8, Jolanda van Leeuwen1, Nydia van Dyk1, Zhen-Yuan Lin9, Elena Kuzmin5, Justin Nelson10, Jeff S Piotrowski11, Tharan Srikumar12, Sondra Bahr1, Yiqun Chen1, Raamesh Deshpande3, Christoph F Kurat1, Sheena C Li11, Zhijian Li1, Mojca Mattiazzi Usaj1, Hiroki Okada13, Natasha Pascoe5, Bryan-Joseph San Luis1, Sara Sharifpoor1, Emira Shuteriqi1, Scott W Simpkins10, Jamie Snider1, Harsha Garadi Suresh1, Yizhao Tan1, Hongwei Zhu1, Noel Malod-Dognin14, Vuk Janjic15, Natasa Przulj16, Olga G Troyanskaya17, Igor Stagljar18, Tian Xia19, Yoshikazu Ohya13, Anne-Claude Gingras20, Brian Raught12, Michael Boutros8, Lars M Steinmetz21, Claire L Moore6, Adam P Rosebrock5, Amy A Caudy5, Chad L Myers22, Brenda Andrews23, Charles Boone24.   

Abstract

We generated a global genetic interaction network for Saccharomyces cerevisiae, constructing more than 23 million double mutants, identifying about 550,000 negative and about 350,000 positive genetic interactions. This comprehensive network maps genetic interactions for essential gene pairs, highlighting essential genes as densely connected hubs. Genetic interaction profiles enabled assembly of a hierarchical model of cell function, including modules corresponding to protein complexes and pathways, biological processes, and cellular compartments. Negative interactions connected functionally related genes, mapped core bioprocesses, and identified pleiotropic genes, whereas positive interactions often mapped general regulatory connections among gene pairs, rather than shared functionality. The global network illustrates how coherent sets of genetic interactions connect protein complex and pathway modules to map a functional wiring diagram of the cell.
Copyright © 2016, American Association for the Advancement of Science.

Entities:  

Mesh：

Substances：

Year:  2016        PMID： 27708008      PMCID： PMC5661885          DOI： 10.1126/science.aaf1420

Source DB:  PubMed          Journal:  Science        ISSN： 0036-8075            Impact factor:   47.728


  117 in total

Review 1.  Principles for the buffering of genetic variation.

Authors:  J L Hartman; B Garvik; L Hartwell
Journal:  Science       Date:  2001-02-09       Impact factor: 47.728

2.  Modular epistasis in yeast metabolism.

Authors:  Daniel Segrè; Alexander Deluna; George M Church; Roy Kishony
Journal:  Nat Genet       Date:  2004-12-12       Impact factor: 38.330

3.  Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae.

Authors:  Mohan Babu; James Vlasblom; Shuye Pu; Xinghua Guo; Chris Graham; Björn D M Bean; Helen E Burston; Franco J Vizeacoumar; Jamie Snider; Sadhna Phanse; Vincent Fong; Yuen Yi C Tam; Michael Davey; Olha Hnatshak; Navgeet Bajaj; Shamanta Chandran; Thanuja Punna; Constantine Christopolous; Victoria Wong; Analyn Yu; Gouqing Zhong; Joyce Li; Igor Stagljar; Elizabeth Conibear; Shoshana J Wodak; Andrew Emili; Jack F Greenblatt
Journal:  Nature       Date:  2012-09-02       Impact factor: 49.962

Review 4.  The ubiquitin-proteasome system of Saccharomyces cerevisiae.

Authors:  Daniel Finley; Helle D Ulrich; Thomas Sommer; Peter Kaiser
Journal:  Genetics       Date:  2012-10       Impact factor: 4.562

5.  Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.

Authors:  Aravind Subramanian; Pablo Tamayo; Vamsi K Mootha; Sayan Mukherjee; Benjamin L Ebert; Michael A Gillette; Amanda Paulovich; Scott L Pomeroy; Todd R Golub; Eric S Lander; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

6.  Plant-derived antifungal agent poacic acid targets β-1,3-glucan.

Authors:  Jeff S Piotrowski; Hiroki Okada; Fachuang Lu; Sheena C Li; Li Hinchman; Ashish Ranjan; Damon L Smith; Alan J Higbee; Arne Ulbrich; Joshua J Coon; Raamesh Deshpande; Yury V Bukhman; Sean McIlwain; Irene M Ong; Chad L Myers; Charles Boone; Robert Landick; John Ralph; Mehdi Kabbage; Yoshikazu Ohya
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-09       Impact factor: 11.205

7.  Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes.

Authors:  Patrick A Gibney; Charles Lu; Amy A Caudy; David C Hess; David Botstein
Journal:  Proc Natl Acad Sci U S A       Date:  2013-10-28       Impact factor: 11.205

8.  Large-scale protein structure modeling of the Saccharomyces cerevisiae genome.

Authors:  R Sánchez; A Sali
Journal:  Proc Natl Acad Sci U S A       Date:  1998-11-10       Impact factor: 11.205

9.  Genetic interactions reveal the evolutionary trajectories of duplicate genes.

Authors:  Benjamin VanderSluis; Jeremy Bellay; Gabriel Musso; Michael Costanzo; Balázs Papp; Franco J Vizeacoumar; Anastasia Baryshnikova; Brenda Andrews; Charles Boone; Chad L Myers
Journal:  Mol Syst Biol       Date:  2010-11-16       Impact factor: 11.429

10.  InParanoid 7: new algorithms and tools for eukaryotic orthology analysis.

Authors:  Gabriel Ostlund; Thomas Schmitt; Kristoffer Forslund; Tina Köstler; David N Messina; Sanjit Roopra; Oliver Frings; Erik L L Sonnhammer
Journal:  Nucleic Acids Res       Date:  2009-11-05       Impact factor: 16.971
View more
  425 in total

1.  Mapping a diversity of genetic interactions in yeast.

Authors:  Jolanda van Leeuwen; Charles Boone; Brenda J Andrews
Journal:  Curr Opin Syst Biol       Date:  2017-08-12

2.  Prioritizing network communities.

Authors:  Marinka Zitnik; Rok Sosič; Jure Leskovec
Journal:  Nat Commun       Date:  2018-06-29       Impact factor: 14.919

3.  Widespread Cumulative Influence of Small Effect Size Mutations on Yeast Quantitative Traits.

Authors:  Bo Hua; Michael Springer
Journal:  Cell Syst       Date:  2018-12-26       Impact factor: 10.304

4.  Six degrees of depolarization: Comment on "Network science of biological systems at different scales: A review" by Marko Gosak et al.

Authors:  Kyle C A Wedgwood; Leslie S Satin
Journal:  Phys Life Rev       Date:  2018-02-01       Impact factor: 11.025

5.  Molecular Origins of Complex Heritability in Natural Genotype-to-Phenotype Relationships.

Authors:  Christopher M Jakobson; Daniel F Jarosz
Journal:  Cell Syst       Date:  2019-05-01       Impact factor: 10.304

Review 6.  Decanalizing thinking on genetic canalization.

Authors:  Kerry Geiler-Samerotte; Federica M O Sartori; Mark L Siegal
Journal:  Semin Cell Dev Biol       Date:  2018-05-24       Impact factor: 7.727

7.  Quantitative Yeast Genetic Interaction Profiling of Bacterial Effector Proteins Uncovers a Role for the Human Retromer in Salmonella Infection.

Authors:  Kristin L Patrick; Jason A Wojcechowskyj; Samantha L Bell; Morgan N Riba; Tao Jing; Sara Talmage; Pengbiao Xu; Ana L Cabello; Jiewei Xu; Michael Shales; David Jimenez-Morales; Thomas A Ficht; Paul de Figueiredo; James E Samuel; Pingwei Li; Nevan J Krogan; Robert O Watson
Journal:  Cell Syst       Date:  2018-08-01       Impact factor: 10.304

8.  Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9-Cas12a platform.

Authors:  Thomas Gonatopoulos-Pournatzis; Michael Aregger; Kevin R Brown; Shaghayegh Farhangmehr; Ulrich Braunschweig; Henry N Ward; Kevin C H Ha; Alexander Weiss; Maximilian Billmann; Tanja Durbic; Chad L Myers; Benjamin J Blencowe; Jason Moffat
Journal:  Nat Biotechnol       Date:  2020-03-16       Impact factor: 54.908

Review 9.  Genetic Network Complexity Shapes Background-Dependent Phenotypic Expression.

Authors:  Jing Hou; Jolanda van Leeuwen; Brenda J Andrews; Charles Boone
Journal:  Trends Genet       Date:  2018-06-11       Impact factor: 11.639

10.  A marine microbiome antifungal targets urgent-threat drug-resistant fungi.

Authors:  Fan Zhang; Miao Zhao; Doug R Braun; Spencer S Ericksen; Jeff S Piotrowski; Justin Nelson; Jian Peng; Gene E Ananiev; Shaurya Chanana; Kenneth Barns; Jen Fossen; Hiram Sanchez; Marc G Chevrette; Ilia A Guzei; Changgui Zhao; Le Guo; Weiping Tang; Cameron R Currie; Scott R Rajski; Anjon Audhya; David R Andes; Tim S Bugni
Journal:  Science       Date:  2020-11-20       Impact factor: 47.728
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.