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.

References

Oct 1, 1973·Proceedings of the National Academy of Sciences of the United States of America·D Oesterhelt, W Stoeckenius
Sep 25, 1997·Trends in Biochemical Sciences·P Mendes
Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Mar 9, 1999·Bioinformatics·M TomitaC A Hutchison
Mar 17, 1999·Proceedings of the National Academy of Sciences of the United States of America·P TamayoT R Golub
Apr 14, 1999·Proceedings of the National Academy of Sciences of the United States of America·M PellegriniT O Yeates
Jan 11, 2000·Nucleic Acids Research·G D BaderC W Hogue
Jan 11, 2000·Nucleic Acids Research·E WingenderS Urbach
Feb 24, 2001·Nature·D Endy, R Brent
Apr 3, 2001·Nature Biotechnology·H ZhouR Aebersold
Aug 3, 2001·Genome Research·UNKNOWN Gene Ontology Consortium
Sep 12, 2001·Current Opinion in Biotechnology·I Xenarios, D Eisenberg
Oct 6, 2001·Trends in Biotechnology·L M Loew, J C Schaff
Dec 26, 2001·Nucleic Acids Research·Minoru KanehisaAkihiro Nakaya
Jan 10, 2002·Trends in Biotechnology·T ItoM Yoshida
Jul 27, 2002·Annual Review of Genomics and Human Genetics·Alex Gilman, Adam P Arkin
Aug 10, 2002·Bioinformatics·Trey IdekerAndrew F Siegel
Oct 26, 2002·Science·Tong Ihn LeeRichard A Young
Oct 31, 2002·Proceedings of the National Academy of Sciences of the United States of America·Nitin S BaligaLeroy Hood

❮ Previous
Next ❯

Citations

May 22, 2008·Archives of Microbiology·J SoppaC Lange
Aug 26, 2006·Analytical and Bioanalytical Chemistry·Peter SchubertJuergen Kast
May 25, 2010·Analytical and Bioanalytical Chemistry·Angelo D'Alessandro, Lello Zolla
Feb 2, 2008·Applied Microbiology and Biotechnology·Hal Alper, Gregory Stephanopoulos
Mar 28, 2009·Journal of Neurology·Robert H GoertschesUwe K Zettl
Jul 28, 2012·Molecular Genetics and Genomics : MGG·Dong Sub KimSi-Yong Kang
Apr 11, 2013·Molecular Genetics and Genomics : MGG·Zhengyuan WangMakedonka Mitreva
Jun 22, 2011·Human Genetics·Kristen Fortney, Igor Jurisica
Jan 22, 2013·Archives of Virology·Jyoti RanaSanjay Gupta
Nov 3, 2009·Amino Acids·Martina CarducciGianni Cesareni
Jan 8, 2013·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·G DubourgD Raoult
Jun 4, 2013·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·A PfleidererD Raoult
Apr 24, 2010·Functional & Integrative Genomics·Yvan DevauxDaniel R Wagner
Aug 31, 2012·Functional & Integrative Genomics·A JuhászE Balázs
Mar 23, 2012·Journal of Plant Research·María del Pilar Valencia-MoralesRaúl Alvarez-Venegas
Mar 10, 2010·Biogerontology·Emilie ChautardSylvie Ricard-Blum
Jun 25, 2013·Cellular and Molecular Neurobiology·Xing-Gang MaoXiang Zhang
Jul 6, 2006·Chromosome Research : an International Journal on the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology·Mathias Beller, Brian Oliver
Feb 17, 2009·Journal of Structural and Functional Genomics·Ursula PieperAndrej Sali
Sep 18, 2009·Journal of Structural and Functional Genomics·Libusha KellyAndrej Sali
Apr 8, 2011·Journal of Structural and Functional Genomics·Margaret J GabanyiHelen M Berman
Aug 27, 2013·Plant Molecular Biology·Neelam K SarkarAnil Grover
Oct 12, 2012·World Journal of Microbiology & Biotechnology·Manoeli LupatiniLuiz Fernando Würdig Roesch
Oct 25, 2013·Chinese Journal of Integrative Medicine·Zhi-Guo ZhangGary Guishan Xiao
Jan 1, 2013·Applied Biochemistry and Biotechnology·Aihua ZhangXijun Wang
Jan 22, 2009·Cell Biochemistry and Biophysics·Nancy TranWilliam K Kaufmann

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.