article Open AccessTop 1% cited
Integration of biological networks and gene expression data using Cytoscape
Nature Protocols · 2007 · Vol. 2(10) · pp. 2366–2382
Melissa Cline✉(Institut Pasteur)Michael Smoot(La Jolla Bioengineering Institute)Ethan Cerami(Memorial Sloan Kettering Cancer Center)Allan Kuchinsky(Agilent Technologies (United States))Nerius Landys(La Jolla Bioengineering Institute)Christopher T. Workman(Technical University of Denmark)Rowan H. Christmas(Institute for Systems Biology)Iliana Avila-Campilo(Institute for Systems Biology)Michael CreechBenjamin Groß(Memorial Sloan Kettering Cancer Center)Kristina Hanspers(Gladstone Institutes)Ruth Isserlin(University of Toronto)Ryan Kelley(La Jolla Bioengineering Institute)Sarah Killcoyne(Institute for Systems Biology)Samad Lotia(La Jolla Bioengineering Institute)Steven Maere(Ghent University)John H. Morris(University of California, San Francisco)Keiichiro Ono(La Jolla Bioengineering Institute)Vuk Pavlovic(University of Toronto)Alexander R. Pico(Gladstone Institutes)Aditya Vailaya(Diagnostics for the Real World (United States))Pengliang Wang(La Jolla Bioengineering Institute)Annette Adler(Agilent Technologies (United States))Bruce R. Conklin(Gladstone Institutes)Leroy Hood(Institute for Systems Biology)Martin Kuiper(Ghent University)Chris Sander(Memorial Sloan Kettering Cancer Center)Ilya Schmulevich(Institute for Systems Biology)Benno Schwikowski(Institut Pasteur)Guy Warner(Unilever (United Kingdom))Trey Ideker(La Jolla Bioengineering Institute)Gary D. Bader(University of Toronto)
Bioinformatics and Genomic NetworksGene expression and cancer classificationGene Regulatory Network AnalysisComputational biologyBiological networkGene regulatory networkGene ontologyFunctional genomicsGene expression profilingComputer scienceInteraction networkSystems biologyGenomics
MeSH terms
RNA, MessengerSoftwareComputational BiologyGene Expression ProfilingGenomicsProteomicsGene Regulatory Networks
Citations
2,566
FWCI
27.75
field-weighted impact
References
75
Percentile
100%
vs. same field & year
Citations per year
Cited by
Comprehensive Proteomic Analysis of Mesenchymal Stem Cell Exosomes Reveals Modulation of Angiogenesis via Nuclear Factor-KappaB Signaling
Stem Cells · 2016 · 531 citations
UCSF ChimeraX: Meeting modern challenges in visualization and analysis
Protein Science · 2017 · 5,669 citations
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation
PLoS ONE · 2010 · 2,406 citations
BioMart – biological queries made easy
BMC Genomics · 2009 · 1,146 citations
Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap
Nature Protocols · 2019 · 2,080 citations
The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible
Nucleic Acids Research · 2016 · 7,394 citations
MicroRNAs are transported in plasma and delivered to recipient cells by high-density lipoproteins
Nature Cell Biology · 2011 · 2,678 citations
Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation
Immunity · 2014 · 2,133 citations
References
MINT: a Molecular INTeraction database
FEBS Letters · 2001 · 789 citations
Gene Ontology: tool for the unification of biology
Nature Genetics · 2000 · 43,975 citations
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Proceedings of the National Academy of Sciences · 2005 · 55,472 citations
An automated method for finding molecular complexes in large protein interaction networks
BMC Bioinformatics · 2003 · 6,204 citations
GoMiner: a resource for biological interpretation of genomic and proteomic data
Genome biology · 2003 · 1,209 citations
The Importance of Bottlenecks in Protein Networks: Correlation with Gene Essentiality and Expression Dynamics
PLoS Computational Biology · 2007 · 1,026 citations
KEGG: Kyoto Encyclopedia of Genes and Genomes
Nucleic Acids Research · 1999 · 32,330 citations
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Genome Research · 2003 · 53,132 citations
Citation Network
How this paper connects to the literature. Drag to explore, click any node to open that paper.