TheCellMap. org: A Web-Accessible Database for Visualizing and Mining the Global Yeast Genetic Interaction Network

被引：92

作者：

Usaj, Matej ^{[1
]}

Tan, Yizhao ^{[1
]}

Wang, Wen ^{[3
]}

VanderSluis, Benjamin ^{[3
,4
,5
]}

Zou, Albert ^{[1
]}

Myers, Chad L. ^{[3
]}

Costanzo, Michael ^{[1
]}

Andrews, Brenda ^{[1
,2
]}

Boone, Charles ^{[1
,2
]}

机构：

[1] Univ Toronto, Donnelly Ctr, 160 Coll St,Room 13212, Toronto, ON M5S 3E1, Canada

[2] Univ Toronto, Dept Mol Genet, Toronto, ON M5S 3E1, Canada

[3] Univ Minnesota Twin Cities, Dept Comp Sci & Engn, 200 Union St, Minneapolis, MN 55455 USA

[4] Simons Fdn, Simons Ctr Data Anal, New York, NY 10010 USA

[5] Princeton Univ, Lewis Sigler Inst Integrat Genom, Princeton, NJ 08544 USA

来源：

G3-GENES GENOMES GENETICS | 2017年 / 7卷 / 05期

基金：

美国国家卫生研究院; 美国国家科学基金会; 加拿大健康研究院;

关键词：

genetic interactions; genetic network; yeast genetics; synthetic genetic array SGA; SACCHAROMYCES-CEREVISIAE GENOME; SYSTEMATIC IDENTIFICATION; MISSING HERITABILITY; ANNOTATION ERRORS; INTERACTION MAP; CELL; LOCALIZATION; ONTOLOGY; DELETION; MUTANTS;

D O I：

10.1534/g3.117.040220

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Providing access to quantitative genomic data is key to ensure large-scale data validation and promote new discoveries. TheCellMap. org serves as a central repository for storing and analyzing quantitative genetic interaction data produced by genome-scale Synthetic Genetic Array (SGA) experiments with the budding yeast Saccharomyces cerevisiae. In particular, TheCellMap. org allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize subnetworks, using data-driven network layouts in an intuitive and interactive manner.

引用

页码：1539 / 1549

页数：11

共 25 条

[1]

[Anonymous], 2012, SPRING EMBEDDERS FOR

[2] Gene Ontology: tool for the unification of biology [J].

Ashburner, M ;

Ball, CA ;

Blake, JA ;

Botstein, D ;

Butler, H ;

Cherry, JM ;

Davis, AP ;

Dolinski, K ;

Dwight, SS ;

Eppig, JT ;

Harris, MA ;

Hill, DP ;

Issel-Tarver, L ;

Kasarskis, A ;

Lewis, S ;

Matese, JC ;

Richardson, JE ;

Ringwald, M ;

Rubin, GM ;

Sherlock, G .

NATURE GENETICS, 2000, 25 (01) :25-29

[3] Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae [J].

Atias, Nir ;

Kupiec, Martin ;

Sharan, Roded .

NUCLEIC ACIDS RESEARCH, 2016, 44 (05) :e50

[4] Systematic Functional Annotation and Visualization of Biological Networks [J].

Baryshnikova, Anastasia .

CELL SYSTEMS, 2016, 2 (06) :412-421

[5]

Baryshnikova A, 2010, NAT METHODS, V7, P1017, DOI [10.1038/nmeth.1534, 10.1038/NMETH.1534]

[6]

Ben-Shitrit T, 2012, NAT METHODS, V9, P373, DOI [10.1038/NMETH.1890, 10.1038/nmeth.1890]

[7] Genetic interactions contribute less than additive effects to quantitative trait variation in yeast [J].

Bloom, Joshua S. ;

Kotenko, Iulia ;

Sadhu, Meru J. ;

Treusch, Sebastian ;

Albert, Frank W. ;

Kruglyak, Leonid .

NATURE COMMUNICATIONS, 2015, 6

[8] Finding the sources of missing heritability in a yeast cross [J].

Bloom, Joshua S. ;

Ehrenreich, Ian M. ;

Loo, Wesley T. ;

Thuy-Lan Vo Lite ;

Kruglyak, Leonid .

NATURE, 2013, 494 (7436) :234-237

[9] A global genetic interaction network maps a wiring diagram of cellular function [J].

Costanzo, Michael ;

VanderSluis, Benjamin ;

Koch, Elizabeth N. ;

Baryshnikova, Anastasia ;

Pons, Carles ;

Tan, Guihong ;

Wang, Wen ;

Usaj, Matej ;

Hanchard, Julia ;

Lee, Susan D. ;

Pelechano, Vicent ;

Styles, Erin B. ;

Billmann, Maximilian ;

van Leeuwen, Jolanda ;

van Dyk, Nydia ;

Lin, Zhen-Yuan ;

Kuzmin, Elena ;

Nelson, Justin ;

Piotrowski, Jeff S. ;

Srikumar, Tharan ;

Bahr, Sondra ;

Chen, Yiqun ;

Deshpande, Raamesh ;

Kurat, Christoph F. ;

Li, Sheena C. ;

Li, Zhijian ;

Usaj, Mojca Mattiazzi ;

Okada, Hiroki ;

Pascoe, Natasha ;

San Luis, Bryan-Joseph ;

Sharifpoor, Sara ;

Shuteriqi, Emira ;

Simpkins, Scott W. ;

Snider, Jamie ;

Suresh, Harsha Garadi ;

Tan, Yizhao ;

Zhu, Hongwei ;

Malod-Dognin, Noel ;

Janjic, Vuk ;

Przulj, Natasa ;

Troyanskaya, Olga G. ;

Stagljar, Igor ;

Xia, Tian ;

Ohya, Yoshikazu ;

Gingras, Anne-Claude ;

Raught, Brian ;

Boutros, Michael ;

Steinmetz, Lars M. ;

Moore, Claire L. ;

Rosebrock, Adam P. .

SCIENCE, 2016, 353 (6306)

[10] Charting the genetic interaction map of a cell [J].

Costanzo, Michael ;

Baryshnikova, Anastasia ;

Myers, Chad L. ;

Andrews, Brenda ;

Boone, Charles .

CURRENT OPINION IN BIOTECHNOLOGY, 2011, 22 (01) :66-74

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