From E-MAPs to module maps: dissecting quantitative genetic interactions using physical interactions

被引：53

作者：

Ulitsky, Igor ^{[1
]}

Shlomi, Tomer ^{[1
]}

Kupiec, Martin ^{[2
]}

Shamir, Ron ^{[1
]}

机构：

[1] Tel Aviv Univ, Sch Comp Sci, IL-69978 Ramat Aviv, Israel

[2] Tel Aviv Univ, Dept Mol Microbiol & Biotechnol, IL-69978 Ramat Aviv, Israel

来源：

MOLECULAR SYSTEMS BIOLOGY | 2008年 / 4卷 / 1期

关键词：

data integration; gene modules; genetic interactions; protein interaction networks;

D O I：

10.1038/msb.2008.42

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Recent technological breakthroughs allow the quantification of hundreds of thousands of genetic interactions (GIs) in Saccharomyces cerevisiae. The interpretation of these data is often difficult, but it can be improved by the joint analysis of GIs along with complementary data types. Here, we describe a novel methodology that integrates genetic and physical interaction data. We use our method to identify a collection of functional modules related to chromosomal biology and to investigate the relations among them. We show how the resulting map of modules provides clues for the elucidation of function both at the level of individual genes and at the level of functional modules.

引用

页数：12

共 58 条

[1] A genome-wide screen for Saccharomyces cerevisiae deletion mutants that affect telomere length [J].

Askree, SH ;

Yehuda, T ;

Smolikov, S ;

Gurevich, R ;

Hawk, J ;

Coker, C ;

Krauskopf, A ;

Kupiec, M ;

McEachern, MJM .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (23) :8658-8663

[2] Purification of active TFIID from Saccharomyces cerevisiae -: Extensive promoter contacts and co-activator function [J].

Auty, R ;

Steen, H ;

Myers, LC ;

Persinger, J ;

Bartholomew, B ;

Gygi, SP ;

Buratowski, S .

JOURNAL OF BIOLOGICAL CHEMISTRY, 2004, 279 (48) :49973-49981

[3] Functional maps of protein complexes from quantitative genetic interaction data [J].

Bandyopadhyay, Sourav ;

Kelley, Ryan ;

Krogan, Nevan J. ;

Ideker, Trey .

PLOS COMPUTATIONAL BIOLOGY, 2008, 4 (04)

[4]

Bauer A, 1996, J CELL SCI, V109, P1575

[5] Integrating physical and genetic maps: from genomes to interaction networks [J].

Beyer, Andreas ;

Bandyopadhyay, Sourav ;

Ideker, Trey .

NATURE REVIEWS GENETICS, 2007, 8 (09) :699-710

[6]

Bilmes J., 1997, GENTLE TUTORIAL EM A

[7] The Bre5/Ubp3 ubiquitin protease complex from budding yeast contributes to the cellular response to DNA damage [J].

Bilsland, Elizabeth ;

Hult, Malin ;

Bell, Stephen D. ;

Sunnerhagen, Per ;

Downs, Jessica A. .

DNA REPAIR, 2007, 6 (10) :1471-1484

[8] Evaluation of clustering algorithms for protein-protein interaction networks [J].

Brohee, Sylvain ;

van Helden, Jacques .

BMC BIOINFORMATICS, 2006, 7 (1)

[9] Global analysis of gene function in yeast by quantitative phenotypic profiling [J].

Brown, James A. ;

Sherlock, Gavin ;

Myers, Chad L. ;

Burrows, Nicola M. ;

Deng, Changchun ;

Wu, H. Irene ;

McCann, Kelly E. ;

Troyanskaya, Olga G. ;

Brown, J. Martin .

MOLECULAR SYSTEMS BIOLOGY, 2006, 2 (1) :2006.0001

[10] SGD:: Saccharomyces Genome Database [J].

Cherry, JM ;

Adler, C ;

Ball, C ;

Chervitz, SA ;

Dwight, SS ;

Hester, ET ;

Jia, YK ;

Juvik, G ;

Roe, T ;

Schroeder, M ;

Weng, SA ;

Botstein, D .

NUCLEIC ACIDS RESEARCH, 1998, 26 (01) :73-79

← 1 2 3 4 5 6 →