Literature DB >> 30901552

Global Genetic Networks and the Genotype-to-Phenotype Relationship.

Michael Costanzo1, Elena Kuzmin2, Jolanda van Leeuwen3, Barbara Mair4, Jason Moffat5, Charles Boone6, Brenda Andrews7.   

Abstract

Genetic interactions identify combinations of genetic variants that impinge on phenotype. With whole-genome sequence information available for thousands of individuals within a species, a major outstanding issue concerns the interpretation of allelic combinations of genes underlying inherited traits. In this Review, we discuss how large-scale analyses in model systems have illuminated the general principles and phenotypic impact of genetic interactions. We focus on studies in budding yeast, including the mapping of a global genetic network. We emphasize how information gained from work in yeast translates to other systems, and how a global genetic network not only annotates gene function but also provides new insights into the genotype-to-phenotype relationship.
Copyright © 2019. Published by Elsevier Inc.

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Year:  2019        PMID: 30901552      PMCID: PMC6817365          DOI: 10.1016/j.cell.2019.01.033

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  108 in total

1.  Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile.

Authors:  Maya Schuldiner; Sean R Collins; Natalie J Thompson; Vladimir Denic; Arunashree Bhamidipati; Thanuja Punna; Jan Ihmels; Brenda Andrews; Charles Boone; Jack F Greenblatt; Jonathan S Weissman; Nevan J Krogan
Journal:  Cell       Date:  2005-11-04       Impact factor: 41.582

Review 2.  Emerging and evolving concepts in gene essentiality.

Authors:  Giulia Rancati; Jason Moffat; Athanasios Typas; Norman Pavelka
Journal:  Nat Rev Genet       Date:  2017-10-16       Impact factor: 53.242

3.  Genetic interaction mapping in mammalian cells using CRISPR interference.

Authors:  Dan Du; Assen Roguev; David E Gordon; Meng Chen; Si-Han Chen; Michael Shales; John Paul Shen; Trey Ideker; Prashant Mali; Lei S Qi; Nevan J Krogan
Journal:  Nat Methods       Date:  2017-05-08       Impact factor: 28.547

4.  Dissection of DNA damage responses using multiconditional genetic interaction maps.

Authors:  Aude Guénolé; Rohith Srivas; Kees Vreeken; Ze Zhong Wang; Shuyi Wang; Nevan J Krogan; Trey Ideker; Haico van Attikum
Journal:  Mol Cell       Date:  2012-12-27       Impact factor: 17.970

5.  Exploring genetic suppression interactions on a global scale.

Authors:  Jolanda van Leeuwen; Carles Pons; Joseph C Mellor; Takafumi N Yamaguchi; Helena Friesen; John Koschwanez; Mojca Mattiazzi Ušaj; Maria Pechlaner; Mehmet Takar; Matej Ušaj; Benjamin VanderSluis; Kerry Andrusiak; Pritpal Bansal; Anastasia Baryshnikova; Claire E Boone; Jessica Cao; Atina Cote; Marinella Gebbia; Gene Horecka; Ira Horecka; Elena Kuzmin; Nicole Legro; Wendy Liang; Natascha van Lieshout; Margaret McNee; Bryan-Joseph San Luis; Fatemeh Shaeri; Ermira Shuteriqi; Song Sun; Lu Yang; Ji-Young Youn; Michael Yuen; Michael Costanzo; Anne-Claude Gingras; Patrick Aloy; Chris Oostenbrink; Andrew Murray; Todd R Graham; Chad L Myers; Brenda J Andrews; Frederick P Roth; Charles Boone
Journal:  Science       Date:  2016-11-04       Impact factor: 47.728

6.  Systematic triple-mutant analysis uncovers functional connectivity between pathways involved in chromosome regulation.

Authors:  James E Haber; Hannes Braberg; Qiuqin Wu; Richard Alexander; Julian Haase; Colm Ryan; Zach Lipkin-Moore; Kathleen E Franks-Skiba; Tasha Johnson; Michael Shales; Tineke L Lenstra; Frank C P Holstege; Jeffrey R Johnson; Kerry Bloom; Nevan J Krogan
Journal:  Cell Rep       Date:  2013-06-06       Impact factor: 9.423

Review 7.  Integrating genetic approaches into the discovery of anticancer drugs.

Authors:  L H Hartwell; P Szankasi; C J Roberts; A W Murray; S H Friend
Journal:  Science       Date:  1997-11-07       Impact factor: 47.728

Review 8.  Missing heritability and strategies for finding the underlying causes of complex disease.

Authors:  Evan E Eichler; Jonathan Flint; Greg Gibson; Augustine Kong; Suzanne M Leal; Jason H Moore; Joseph H Nadeau
Journal:  Nat Rev Genet       Date:  2010-06       Impact factor: 53.242

9.  Cytoscape 2.8: new features for data integration and network visualization.

Authors:  Michael E Smoot; Keiichiro Ono; Johannes Ruscheinski; Peng-Liang Wang; Trey Ideker
Journal:  Bioinformatics       Date:  2010-12-12       Impact factor: 6.937

10.  Genetic interactions involving five or more genes contribute to a complex trait in yeast.

Authors:  Matthew B Taylor; Ian M Ehrenreich
Journal:  PLoS Genet       Date:  2014-05-01       Impact factor: 5.917

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  54 in total

1.  Modeling DNA trapping of anticancer therapeutic targets using missense mutations identifies dominant synthetic lethal interactions.

Authors:  Akil Hamza; Leanne Amitzi; Lina Ma; Maureen R M Driessen; Nigel J O'Neil; Philip Hieter
Journal:  Proc Natl Acad Sci U S A       Date:  2021-04-06       Impact factor: 11.205

2.  Genetic Interaction Network Interpretation: A Tidy Data Science Perspective.

Authors:  Lulu Jiang; Hai Fang
Journal:  Methods Mol Biol       Date:  2021

Review 3.  In vivo functional screening for systems-level integrative cancer genomics.

Authors:  Julia Weber; Christian J Braun; Dieter Saur; Roland Rad
Journal:  Nat Rev Cancer       Date:  2020-07-07       Impact factor: 60.716

4.  A Genetic Map of the Response to DNA Damage in Human Cells.

Authors:  Michele Olivieri; Tiffany Cho; Alejandro Álvarez-Quilón; Kejiao Li; Matthew J Schellenberg; Michal Zimmermann; Nicole Hustedt; Silvia Emma Rossi; Salomé Adam; Henrique Melo; Anne Margriet Heijink; Guillermo Sastre-Moreno; Nathalie Moatti; Rachel K Szilard; Andrea McEwan; Alexanda K Ling; Almudena Serrano-Benitez; Tajinder Ubhi; Sumin Feng; Judy Pawling; Irene Delgado-Sainz; Michael W Ferguson; James W Dennis; Grant W Brown; Felipe Cortés-Ledesma; R Scott Williams; Alberto Martin; Dongyi Xu; Daniel Durocher
Journal:  Cell       Date:  2020-07-09       Impact factor: 41.582

5.  Exploring genetic interaction manifolds constructed from rich single-cell phenotypes.

Authors:  Thomas M Norman; Max A Horlbeck; Joseph M Replogle; Alex Y Ge; Albert Xu; Marco Jost; Luke A Gilbert; Jonathan S Weissman
Journal:  Science       Date:  2019-08-08       Impact factor: 47.728

6.  Diagnostic high-throughput sequencing of 2396 patients with bleeding, thrombotic, and platelet disorders.

Authors:  Kate Downes; Karyn Megy; Daniel Duarte; Minka Vries; Johanna Gebhart; Stefanie Hofer; Olga Shamardina; Sri V V Deevi; Jonathan Stephens; Rutendo Mapeta; Salih Tuna; Namir Al Hasso; Martin W Besser; Nichola Cooper; Louise Daugherty; Nick Gleadall; Daniel Greene; Matthias Haimel; Howard Martin; Sofia Papadia; Shoshana Revel-Vilk; Suthesh Sivapalaratnam; Emily Symington; Will Thomas; Chantal Thys; Alexander Tolios; Christopher J Penkett; Willem H Ouwehand; Stephen Abbs; Michael A Laffan; Ernest Turro; Ilenia Simeoni; Andrew D Mumford; Yvonne M C Henskens; Ingrid Pabinger; Keith Gomez; Kathleen Freson
Journal:  Blood       Date:  2019-12-05       Impact factor: 22.113

7.  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

8.  The chloroplast metalloproteases VAR2 and EGY1 act synergistically to regulate chloroplast development in Arabidopsis.

Authors:  Yafei Qi; Xiaomin Wang; Pei Lei; Huimin Li; Liru Yan; Jun Zhao; Jingjing Meng; Jingxia Shao; Lijun An; Fei Yu; Xiayan Liu
Journal:  J Biol Chem       Date:  2019-12-13       Impact factor: 5.157

Review 9.  Retention of duplicated genes in evolution.

Authors:  Elena Kuzmin; John S Taylor; Charles Boone
Journal:  Trends Genet       Date:  2021-07-20       Impact factor: 11.639

Review 10.  Genetics animates structure: leveraging genetic interactions to study the dynamics of ribosome biogenesis.

Authors:  Joshua J Black; Arlen W Johnson
Journal:  Curr Genet       Date:  2021-04-12       Impact factor: 3.886

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