Cytoscape: a software environment for integrated models of biomolecular interaction networks

Genome Research
Paul ShannonTrey Ideker

Abstract

Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.

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May 18, 2013·Database : the Journal of Biological Databases and Curation·Anuradha PujarLukas A Mueller
Jun 27, 2013·Database : the Journal of Biological Databases and Curation·Xiaoping LiuXing-Ming Zhao
Jun 26, 2013·Database : the Journal of Biological Databases and Curation·Stephen L MathiasTudor I Oprea
Nov 15, 2007·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Shusei SatoSatoshi Tabata
Apr 11, 2013·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Sung Don LimCheol Seong Jang
Jan 10, 2012·Genome Biology and Evolution·Elizabeth Skippington, Mark A Ragan
Dec 10, 2009·Human Molecular Genetics·Sulin WuThomas A Drake
Jun 12, 2013·Human Molecular Genetics·Dorothee NicklesSergio E Baranzini
Sep 13, 2008·The Journal of Antimicrobial Chemotherapy·Alejandro DelgadoJohn E Gustafson
Apr 27, 2010·Molecular Biology and Evolution·Kyung Mo Kim, Gustavo Caetano-Anollés
Oct 7, 2010·Molecular Biology and Evolution·Ludovica MontanucciJaume Bertranpetit
Sep 15, 2012·Molecular Biology and Evolution·Alexandr BezginovElisabeth R M Tillier
May 11, 2013·Molecular Biology and Evolution·Yan LiYa-Ping Zhang
Jun 25, 2004·Nucleic Acids Research·Brian P KelleyTrey Ideker
Jun 25, 2004·Nucleic Acids Research·Kyungsook HanHaemoon Jung
Dec 21, 2004·Nucleic Acids Research·C AlfaranoC W V Hogue
Dec 21, 2004·Nucleic Acids Research·Luc J SminkNathan Goodman
Feb 9, 2006·Nucleic Acids Research·Björn TitzPeter Uetz
Jul 18, 2006·Nucleic Acids Research·Michael BaitalukAmarnath Gupta
Nov 30, 2006·Nucleic Acids Research·Magesh JayapandianH V Jagadish
Dec 16, 2006·Nucleic Acids Research·Erin M HulbertNathan Goodman
Dec 1, 2006·Nucleic Acids Research·H Craig MakTrey Ideker
Dec 6, 2006·Nucleic Acids Research·S KerrienHenning Hermjakob
Nov 15, 2007·Nucleic Acids Research·Bobby-Joe BreitkreutzMike Tyers
Jun 26, 2007·Nucleic Acids Research·Zhenjun HuCharles DeLisi
Jun 23, 2007·Nucleic Acids Research·Purvesh KhatriSorin Draghici
Oct 19, 2007·Nucleic Acids Research·Chong SuJohn Parkinson
May 15, 2008·Nucleic Acids Research·Shujiro OkudaMinoru Kanehisa
Jun 6, 2008·Nucleic Acids Research·Sylvain BrohéeJacques van Helden
Sep 30, 2008·Nucleic Acids Research·Supat ThongjueaApichart Vanavichit
Oct 10, 2008·Nucleic Acids Research·Yoshinobu IgarashiAlexey M Eroshkin
Nov 4, 2008·Nucleic Acids Research·V Glenn TarceaH V Jagadish
Oct 23, 2008·Nucleic Acids Research·Lars J JensenChristian von Mering
Nov 4, 2008·Nucleic Acids Research·Su-Jun LiRong Zeng
Nov 14, 2008·Nucleic Acids Research·Eduardo Andres LeonDavid Juan
Feb 4, 2009·Nucleic Acids Research·Javier CarreraAlfonso Jaramillo
Mar 11, 2009·Nucleic Acids Research·Gregory R StuartMicheline K Strand
May 21, 2009·Nucleic Acids Research·Pablo MinguezJoaquín Dopazo
Jun 6, 2009·Nucleic Acids Research·Sharon BrucknerRoded Sharan
Nov 3, 2009·Nucleic Acids Research·Judice L Y KohCharles Boone
Oct 24, 2009·Nucleic Acids Research·B ArandaHenning Hermjakob
Nov 13, 2010·Nucleic Acids Research·Joachim von EichbornRobert Preissner
Nov 13, 2010·Nucleic Acids Research·Ethan G CeramiChris Sander
Nov 13, 2010·Nucleic Acids Research·Atanas KamburovRalf Herwig
Nov 26, 2010·Nucleic Acids Research·Arnon PazRon Shamir
May 7, 2010·Nucleic Acids Research·Ludovic CottretFabien Jourdan
May 21, 2010·Nucleic Acids Research·Marija CvijovicJens Nielsen
May 29, 2010·Nucleic Acids Research·Divya SardanaAnil G Jegga
Jun 12, 2010·Nucleic Acids Research·Y-T WangU-C Yang
Aug 21, 2010·Nucleic Acids Research·Morana VitezicCarsten O Daub
Sep 24, 2010·Nucleic Acids Research·Melissa A MullenPhilip C Bevilacqua
Sep 21, 2010·Nucleic Acids Research·Emilie ChautardSylvie Ricard-Blum
Nov 4, 2010·Nucleic Acids Research·Damian SzklarczykChristian von Mering
Dec 6, 2011·Nucleic Acids Research·Lydie LaneAmos Bairoch
Jan 3, 2012·Nucleic Acids Research·Christina BackesHans-Peter Lenhof
Jun 22, 2011·Nucleic Acids Research·Anna StinconeFrancesco Falciani
Nov 28, 2012·Nucleic Acids Research·Yutaka SatoYoshiaki Nagamura
Nov 30, 2012·Nucleic Acids Research·Gabriella RusticiUgis Sarkans
May 30, 2012·Nucleic Acids Research·Yoan RenaudVincent Mirouse
May 23, 2012·Nucleic Acids Research·Masaaki KoteraSusumu Goto
Jun 7, 2012·Nucleic Acids Research·Jean-Philippe GagnéGuy G Poirier
Oct 9, 2012·Nucleic Acids Research·Maneesha AluruSrinivas Aluru
Oct 25, 2012·Nucleic Acids Research·Allan Peter DavisCarolyn J Mattingly
May 15, 2013·Nucleic Acids Research·Noemi del-ToroHenning Hermjakob
Aug 13, 2013·Nucleic Acids Research·Gautier StollOlivier Delattre
Dec 12, 2012·Nephrology, Dialysis, Transplantation : Official Publication of the European Dialysis and Transplant Association - European Renal Association·Francesco PesceFrancesco Paolo Schena
Dec 14, 2011·Toxicological Sciences : an Official Journal of the Society of Toxicology·Joanna ParkinsonLorna Ewart
May 30, 2012·Toxicological Sciences : an Official Journal of the Society of Toxicology·Jay S SchneiderRajanikanth Vadigepalli
Dec 18, 2012·Toxicological Sciences : an Official Journal of the Society of Toxicology·Peter T TheunissenAldert H Piersma
Jan 21, 2010·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·A BerryR P Donn
Nov 11, 2011·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Alessandro PandiniJens Kleinjung
Apr 18, 2009·Cognitive and Behavioral Neurology : Official Journal of the Society for Behavioral and Cognitive Neurology·Alan J LernerPeter J Thomas
Dec 19, 2008·Journal of the Royal Society, Interface·Joana P GonçalvesAndré X C N Valente
Jul 12, 2013·Proceedings. Biological Sciences·Sebastian BoltañaS Mackenzie
Sep 17, 2008·Genes & Development·Natalia J MartinezAlbertha J M Walhout
Dec 20, 2008·Genes & Development·Sorina C PopescuSavithramma P Dinesh-Kumar
Apr 18, 2009·Genome Research·H Craig MakTrey Ideker
Feb 28, 2009·Genome Research·Andrey Alexeyenko, Erik L L Sonnhammer
Aug 22, 2009·Genome Research·Elisabeth R M Tillier, Robert L Charlebois
Feb 18, 2011·Genome Research·Lesley T Macneil, Albertha J M Walhout
Nov 3, 2010·Genome Research·Ruth A Swanson-WagnerNathan M Springer
Aug 10, 2011·Genome Research·Kevin DrewRichard Bonneau
Feb 22, 2012·Genome Research·Vincenzo Alessandro GennarinoSandro Banfi
Mar 30, 2013·Genome Research·Ashlyn D RitterAlbertha J M Walhout
Mar 3, 2004·Genome Research·Susanne PrinzTimothy Galitski
Nov 3, 2004·Genome Research·Nitin S BaligaWailap Victor Ng