Integration of biological networks and gene expression data using Cytoscape

By Melissa S. Cline, Michael E. Smoot, Ethan G. Cerami, Allan Kuchinsky, Nerius Landys, Chris Workman, R. Christmas, Iliana Avila-Campilo, Michael L. Creech, Benjamin E. Gross and 22 more. Nature Protocols, 2007

2,523 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0d811afe55b939c9672e164f37957e9364434c84

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Citations in the corpus

Cytoscape StringApp: Network Analysis and Visualization of Proteomics Data (2018, background): “The Cytoscape software 2,3 , on the other hand, is designed to analyze and visualize very large networks and provides much greater flexibility in terms of import of additional data and visualization of these onto networks.”
The BioMart community portal: an innovative alternative to large, centralized data repositories (2015, background): “It also supports many third party packages such as Taverna (2), Galaxy (3), Cytoscape (4) and biomaRt (5), which part of the Bioconductor (6) library.”
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored (2010, methodology): “Cytoscape is a widely used open-source software framework for network visualization and manipulation (54,55); it can be very ﬂexibly extended, with a rapidly growing number of network-centered manipulation and analysis tools.”
Network-based prediction of human tissue-specific metabolism (2008, methodology): “il/~shlomito/tissue-net ) and can be explored interactively using the freely available Cytoscape softwar”
Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism (2013, positive): “The Period 3–5 and Period 4–6 PFC-MSC Networks (A and B) The period 3–5 (A) and period 4–6 (B) coexpression networks are displayed with the force-directed layout function of Cytoscape using correlation as the edge weight (Cline et al., 2007).”
GPCR-I-TASSER: A hybrid approach to G protein-coupled receptor structure modeling and the application to the human genome (2015, methodology): “Sequence and Structure Networks of Human GPCRs Given the sequence and structural models generated, we pre-sent in Figure 8 a 2D view of the sequence and structure distributions of all 1,026 GPCRs in human prepared using Cytoscape 2.8 (Cline et al., 2007).”
PID: the Pathway Interaction Database (2008, neutral): “Using the BioPAX export, a user can also visualize PID pathways in Cytoscape (http://cytoscape.org) a popular third-party network visualization tool (9).”
More Is Better: Recent Progress in Multi-Omics Data Integration Methods (2017, positive): “Through random sampling approach and iterative calculations, jActiveModules determines the highest-scoring sub-network circuits in a full network of molecular interactions, leading to further biologically interesting discoveries (Cline et al., 2007).”
Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation (2014, methodology): “Networks were visualized in a force-directed layout in Cytoscape, followed with statistical analysis utilizing the plug-in Network Analysis (Cline et al., 2007).”
The BioGRID Interaction Database: 2011 update (2010, methodology): “BioGRID interaction data can also be accessed automatically through biological network visualization applications that include Osprey (26), Cytoscape (27), GeneMania (28) and ProHits (29).”
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation (2010, methodology): “Tools such as Onto-Express [25], the Cytoscape [26] plugin BiNGO [27] and WebGestalt [28] display the hierarchical structure of enriched GO terms.”
iMAT: an integrative metabolic analysis tool (2010, neutral): “…the corresponding enzyme-coding gene, the corresponding gene is considered to be post-transcriptionally up- or downregulated. iMAT provides as output the predicted flux activity state and the corresponding confidence values over all network reactions in both tabular and network visualization forms.”