Network analysis of GWAS data

被引：66

作者：

Leiserson, Mark D. M. ^{[1
,2
]}

Eldridge, Jonathan V. ^{[1
,2
]}

Ramachandran, Sohini ^{[2
,3
]}

Raphael, Benjamin J. ^{[1
,2
]}

机构：

[1] Brown Univ, Dept Comp Sci, Providence, RI 02912 USA

[2] Brown Univ, Ctr Computat Mol Biol, Providence, RI 02912 USA

[3] Brown Univ, Dept Ecol & Evolutionary Biol, Providence, RI 02912 USA

来源：

CURRENT OPINION IN GENETICS & DEVELOPMENT | 2013年 / 23卷 / 06期

基金：

美国国家科学基金会;

关键词：

GENOME-WIDE ASSOCIATION; CANDIDATE DISEASE GENES; PROTEIN-INTERACTION NETWORK; MISSING HERITABILITY; TOPOLOGICAL SIMILARITY; INTERACTOME; PATHWAYS; PRIORITIZATION; VARIANTS; PHENOME;

D O I：

10.1016/j.gde.2013.09.003

中图分类号：

Q2 [细胞生物学];

学科分类号：

071009 ; 090102 ;

摘要：

Genome-wide association studies (GWAS) identify genetic variants that distinguish a control population from a population with a specific trait. Two challenges in GWAS are: (1) identification of the causal variant within a longer haplotype that is associated with the trait; (2) identification of causal variants for polygenic traits that are caused by variants in multiple genes within a pathway. We review recent methods that use information in protein-protein and protein-DNA interaction networks to address these two challenges.

引用

页码：602 / 610

页数：9

共 56 条

[1] A Network-Based Approach to Prioritize Results from Genome-Wide Association Studies [J].

Akula, Nirmala ;

Baranova, Ancha ;

Seto, Donald ;

Solka, Jeffrey ;

Nalls, Michael A. ;

Singleton, Andrew ;

Ferrucci, Luigi ;

Tanaka, Toshiko ;

Bandinelli, Stefania ;

Cho, Yoon Shin ;

Kim, Young Jin ;

Lee, Jong-Young ;

Han, Bok-Ghee ;

McMahon, Francis J. .

PLOS ONE, 2011, 6 (09)

[2] Network-Based Multiple Sclerosis Pathway Analysis with GWAS Data from 15,000 Cases and 30,000 Controls [J].

Baranzini, Sergio E. ;

Khankhanian, Pouya ;

Patsopoulos, Nikolaos A. ;

Li, Michael ;

Stankovich, Jim ;

Cotsapas, Chris ;

Sondergaard, Helle Bach ;

Ban, Maria ;

Barizzone, Nadia ;

Bergamaschi, Laura ;

Booth, David ;

Buck, Dorothea ;

Cavalla, Paola ;

Celius, Elisabeth G. ;

Comabella, Manuel ;

Comi, Giancarlo ;

Compston, Alastair ;

Cournu-Rebeix, Isabelle ;

D'alfonso, Sandra ;

Damotte, Vincent ;

Din, Lennox ;

Dubois, Benedicte ;

Elovaara, Irina ;

Esposito, Federica ;

Fontaine, Bertrand ;

Franke, Andre ;

Goris, An ;

Gourraud, Pierre-Antoine ;

Graetz, Christiane ;

Guerini, Franca R. ;

Guillot-Noel, Lena ;

Hafler, David ;

Hakonarson, Hakon ;

Hall, Per ;

Hamsten, Anders ;

Harbo, Hanne F. ;

Hemmer, Bernhard ;

Hillert, Jan ;

Kemppinen, Anu ;

Kockum, Ingrid ;

Koivisto, Keijo ;

Larsson, Maim ;

Lathrop, Mark ;

Leone, Maurizio ;

Lill, Christina M. ;

Macciardi, Fabio ;

Martin, Roland ;

Martinelli, Vittorio ;

Martinelli-Boneschi, Filippo ;

McCauley, Jacob L. .

AMERICAN JOURNAL OF HUMAN GENETICS, 2013, 92 (06) :854-865

[3] Pathway and network-based analysis of genome-wide association studies in multiple sclerosis [J].

Baranzini, Sergio E. ;

Galwey, Nicholas W. ;

Wang, Joanne ;

Khankhanian, Pouya ;

Lindberg, Raija ;

Pelletier, Daniel ;

Wu, Wen ;

Uitdehaag, Bernard M. J. ;

Kappos, Ludwig ;

Polman, Chris H. ;

Matthews, Paul M. ;

Hauser, Stephen L. ;

Gibson, Rachel A. ;

Oksenberg, Jorge R. ;

Barnes, Michael R. .

HUMAN MOLECULAR GENETICS, 2009, 18 (11) :2078-2090

[4] ResponseNet2.0: revealing signaling and regulatory pathways connecting your proteins and genes-now with human data [J].

Basha, Omer ;

Tirman, Shoval ;

Eluk, Amir ;

Yeger-Lotem, Esti .

NUCLEIC ACIDS RESEARCH, 2013, 41 (W1) :W198-W203

[5] The anatomy of a large-scale hypertextual Web search engine [J].

Brin, S ;

Page, L .

COMPUTER NETWORKS AND ISDN SYSTEMS, 1998, 30 (1-7) :107-117

[6] Automated Network Analysis Identifies Core Pathways in Glioblastoma [J].

Cerami, Ethan ;

Demir, Emek ;

Schultz, Nikolaus ;

Taylor, Barry S. ;

Sander, Chris .

PLOS ONE, 2010, 5 (02)

[7] Uncover disease genes by maximizing information flow in the phenome-interactome network [J].

Chen, Yong ;

Jiang, Tao ;

Jiang, Rui .

BIOINFORMATICS, 2011, 27 (13) :I167-I176

[8] Reactome: a database of reactions, pathways and biological processes [J].

Croft, David ;

O'Kelly, Gavin ;

Wu, Guanming ;

Haw, Robin ;

Gillespie, Marc ;

Matthews, Lisa ;

Caudy, Michael ;

Garapati, Phani ;

Gopinath, Gopal ;

Jassal, Bijay ;

Jupe, Steven ;

Kalatskaya, Irina ;

Mahajan, Shahana ;

May, Bruce ;

Ndegwa, Nelson ;

Schmidt, Esther ;

Shamovsky, Veronica ;

Yung, Christina ;

Birney, Ewan ;

Hermjakob, Henning ;

D'Eustachio, Peter ;

Stein, Lincoln .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D691-D697

[9] An integrated encyclopedia of DNA elements in the human genome [J].

Dunham, Ian ;

Kundaje, Anshul ;

Aldred, Shelley F. ;

Collins, Patrick J. ;

Davis, CarrieA. ;

Doyle, Francis ;

Epstein, Charles B. ;

Frietze, Seth ;

Harrow, Jennifer ;

Kaul, Rajinder ;

Khatun, Jainab ;

Lajoie, Bryan R. ;

Landt, Stephen G. ;

Lee, Bum-Kyu ;

Pauli, Florencia ;

Rosenbloom, Kate R. ;

Sabo, Peter ;

Safi, Alexias ;

Sanyal, Amartya ;

Shoresh, Noam ;

Simon, Jeremy M. ;

Song, Lingyun ;

Trinklein, Nathan D. ;

Altshuler, Robert C. ;

Birney, Ewan ;

Brown, James B. ;

Cheng, Chao ;

Djebali, Sarah ;

Dong, Xianjun ;

Dunham, Ian ;

Ernst, Jason ;

Furey, Terrence S. ;

Gerstein, Mark ;

Giardine, Belinda ;

Greven, Melissa ;

Hardison, Ross C. ;

Harris, Robert S. ;

Herrero, Javier ;

Hoffman, Michael M. ;

Iyer, Sowmya ;

Kellis, Manolis ;

Khatun, Jainab ;

Kheradpour, Pouya ;

Kundaje, Anshul ;

Lassmann, Timo ;

Li, Qunhua ;

Lin, Xinying ;

Marinov, Georgi K. ;

Merkel, Angelika ;

Mortazavi, Ali .

NATURE, 2012, 489 (7414) :57-74

[10] VIEWPOINT Missing heritability and strategies for finding the underlying causes of complex disease [J].

Eichler, Evan E. ;

Flint, Jonathan ;

Gibson, Greg ;

Kong, Augustine ;

Leal, Suzanne M. ;

Moore, Jason H. ;

Nadeau, Joseph H. .

NATURE REVIEWS GENETICS, 2010, 11 (06) :446-450

← 1 2 3 4 5 6 →