GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop

被引:476
作者
Montojo, J.
Zuberi, K.
Rodriguez, H.
Kazi, F.
Wright, G.
Donaldson, S. L.
Morris, Q. [1 ]
Bader, G. D.
机构
[1] Univ Toronto, Banting & Best Dept Med Res, Toronto, ON M5S 3E1, Canada
关键词
INTEGRATION;
D O I
10.1093/bioinformatics/btq562
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
The GeneMANIA Cytoscape plugin brings fast gene function prediction capabilities to the desktop. GeneMANIA identifies the most related genes to a query gene set using a guilt-by-association approach. The plugin uses over 800 networks from six organisms and each related gene is traceable to the source network used to make the prediction. Users may add their own interaction networks and expression profile data to complement or override the default data.
引用
收藏
页码:2927 / 2928
页数:2
相关论文
共 9 条
[1]   NCBI GEO: archive for high-throughput functional genomic data [J].
Barrett, Tanya ;
Troup, Dennis B. ;
Wilhite, Stephen E. ;
Ledoux, Pierre ;
Rudnev, Dmitry ;
Evangelista, Carlos ;
Kim, Irene F. ;
Soboleva, Alexandra ;
Tomashevsky, Maxim ;
Marshall, Kimberly A. ;
Phillippy, Katherine H. ;
Sherman, Patti M. ;
Muertter, Rolf N. ;
Edgar, Ron .
NUCLEIC ACIDS RESEARCH, 2009, 37 :D885-D890
[2]   The BioGRID interaction database:: 2008 update [J].
Breitkreutz, Bobby-Joe ;
Stark, Chris ;
Reguly, Teresa ;
Boucher, Lorrie ;
Breitkreutz, Ashton ;
Livstone, Michael ;
Oughtred, Rose ;
Lackner, Daniel H. ;
Bahler, Jurg ;
Wood, Valerie ;
Dolinski, Kara ;
Tyers, Mike .
NUCLEIC ACIDS RESEARCH, 2008, 36 :D637-D640
[3]   Online predicted human interaction database [J].
Brown, KR ;
Jurisica, I .
BIOINFORMATICS, 2005, 21 (09) :2076-2082
[4]   A Compendium of Potential Biomarkers of Pancreatic Cancer [J].
Harsha, H. C. ;
Kandasamy, Kumaran ;
Ranganathan, Prathibha ;
Rani, Sandhya ;
Ramabadran, Subhashri ;
Gollapudi, Sashikanth ;
Balakrishnan, Lavanya ;
Dwivedi, Sutopa B. ;
Telikicherla, Deepthi ;
Selvan, Lakshmi Dhevi N. ;
Goel, Renu ;
Mathivanan, Suresh ;
Marimuthu, Arivusudar ;
Kashyap, Manoj ;
Vizza, Robert F. ;
Mayer, Robert J. ;
DeCaprio, James A. ;
Srivastava, Sudhir ;
Hanash, Samir M. ;
Hruban, Ralph H. ;
Pandey, Akhilesh .
PLOS MEDICINE, 2009, 6 (04)
[5]   Fast integration of heterogeneous data sources for predicting gene function with limited annotation [J].
Mostafavi, Sara ;
Morris, Quaid .
BIOINFORMATICS, 2010, 26 (14) :1759-1765
[6]   GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function [J].
Mostafavi, Sara ;
Ray, Debajyoti ;
Warde-Farley, David ;
Grouios, Chris ;
Morris, Quaid .
GENOME BIOLOGY, 2008, 9 (Suppl 1)
[7]   A critical assessment of Mus musculus gene function prediction using integrated genomic evidence [J].
Pena-Castillo, Lourdes ;
Tasan, Murat ;
Myers, Chad L. ;
Lee, Hyunju ;
Joshi, Trupti ;
Zhang, Chao ;
Guan, Yuanfang ;
Leone, Michele ;
Pagnani, Andrea ;
Kim, Wan Kyu ;
Krumpelman, Chase ;
Tian, Weidong ;
Obozinski, Guillaume ;
Qi, Yanjun ;
Mostafavi, Sara ;
Lin, Guan Ning ;
Berriz, Gabriel F. ;
Gibbons, Francis D. ;
Lanckriet, Gert ;
Qiu, Jian ;
Grant, Charles ;
Barutcuoglu, Zafer ;
Hill, David P. ;
Warde-Farley, David ;
Grouios, Chris ;
Ray, Debajyoti ;
Blake, Judith A. ;
Deng, Minghua ;
Jordan, Michael I. ;
Noble, William S. ;
Morris, Quaid ;
Klein-Seetharaman, Judith ;
Bar-Joseph, Ziv ;
Chen, Ting ;
Sun, Fengzhu ;
Troyanskaya, Olga G. ;
Marcotte, Edward M. ;
Xu, Dong ;
Hughes, Timothy R. ;
Roth, Frederick P. .
GENOME BIOLOGY, 2008, 9 (Suppl 1)
[8]   Cytoscape: A software environment for integrated models of biomolecular interaction networks [J].
Shannon, P ;
Markiel, A ;
Ozier, O ;
Baliga, NS ;
Wang, JT ;
Ramage, D ;
Amin, N ;
Schwikowski, B ;
Ideker, T .
GENOME RESEARCH, 2003, 13 (11) :2498-2504
[9]   The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function [J].
Warde-Farley, David ;
Donaldson, Sylva L. ;
Comes, Ovi ;
Zuberi, Khalid ;
Badrawi, Rashad ;
Chao, Pauline ;
Franz, Max ;
Grouios, Chris ;
Kazi, Farzana ;
Lopes, Christian Tannus ;
Maitland, Anson ;
Mostafavi, Sara ;
Montojo, Jason ;
Shao, Quentin ;
Wright, George ;
Bader, Gary D. ;
Morris, Quaid .
NUCLEIC ACIDS RESEARCH, 2010, 38 :W214-W220