The Cytoscape app article collection

Pico, Alexander R.; Bader, Gary D.; Demchak, Barry; Guitart, Oriol; Hull, Timothy; Longabaugh, William J.R.; Lopes, Christian; Lotia, Samad; Molenaar, Piet; Montojo, Jason; Morris, John H.; Ono, Keiichiro; Schwikowski, Benno; Welker, David; Ideker, Trey

doi:10.12688/f1000research.4642.1

Cited by 9 publications

(10 citation statements)

References 5 publications

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“…Network analyses and visualization were performed using Cytoscape 80 – 82 . Clustering calculations and interactive heatmaps of effector targets were generated by custom made scripts using heatmaply v0.7.0 package for R language.…”

Section: Methodsmentioning

confidence: 99%

“…We set a cut-off of Log2 +1 and −1 for up- and down-regulation and extracted a set of DEGs for each time point for DC3000 hrpA − and DC3000 for dynamic PPI network and dynamic subnetwork analyses. These time-specific up- and down-regulated genes were utilized as “node attribute” to visualize dynamic AI-1 MAIN using Cytoscape 80 – 82 . The extracted DEGs at each time point and static PPI network, AI-1 MAIN were utilized to identify 13 subnetworks (set of protein-protein pairs as previously described in Wang et al .…”

Section: Methodsmentioning

confidence: 99%

“…We subjected 104 differentially expressed 1° effector targets to 5,664 edges of AI-1 MAIN to identify the interacting partners of effector targets (2°effector targets) that are also DEGs either in DC3000 hrpA − and DC3000. These extracted 1° and 2° effector target nodes were used as “node attribute” to visualize dynamic AI-1 MAIN using Cytoscape 80 – 82 . Gene Ontology (GO) enrichment analysis on genes corresponding to effector targets and 2° effector targets was done using DAVID Functional Annotation Bioinformatics Microarray Analysis 84 .…”

Section: Methodsmentioning

confidence: 99%

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Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity

Mishra

Sun

Ahmed

et al. 2017

Sci Rep

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The universal nature of networks’ structural and physical properties across diverse systems offers a better prospect to elucidate the interplay between a system and its environment. In the last decade, several large-scale transcriptome and interactome studies were conducted to understand the complex and dynamic nature of interactions between Arabidopsis and its bacterial pathogen, Pseudomonas syringae pv. tomato DC3000. We took advantage of these publicly available datasets and performed “-omics”-based integrative, and network topology analyses to decipher the transcriptional and protein-protein interaction activities of effector targets. We demonstrated that effector targets exhibit shorter distance to differentially expressed genes (DEGs) and possess increased information centrality. Intriguingly, effector targets are differentially expressed in a sequential manner and make for 1% of the total DEGs at any time point of infection with virulent or defense-inducing DC3000 strains. We revealed that DC3000 significantly alters the expression levels of 71% effector targets and their downstream physical interacting proteins in Arabidopsis interactome. Our integrative “-omics”-–based analyses identified dynamic complexes associated with MTI and disease susceptibility. Finally, we discovered five novel plant defense players using a systems biology-fueled top-to-bottom approach and demonstrated immune-related functions for them, further validating the power and resolution of our network analyses.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity

Mishra

Sun

Ahmed

et al. 2017

Sci Rep

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“…Cytoscape is a well-established Java-based stand-alone application for analyzing and visualizing networks [ 20 – 22 ]. Cytoscape offers a user-friendly graphical user interface (GUI) for visualizing a given network, and provides an app store at http://apps.cytoscape.org/ from which apps for various systems biology applications can be downloaded [ 23 ]. In addition, software developers can submit new apps to be made available from the Cytoscape App Store, such as [ 11 , 24 – 26 ].…”

Section: Introductionmentioning

confidence: 99%

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research

et al. 2016

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Reproducibility is vital in science. For complex computational methods, it is often necessary, not just to recreate the code, but also the software and hardware environment to reproduce results. Virtual machines, and container software such as Docker, make it possible to reproduce the exact environment regardless of the underlying hardware and operating system. However, workflows that use Graphical User Interfaces (GUIs) remain difficult to replicate on different host systems as there is no high level graphical software layer common to all platforms. GUIdock allows for the facile distribution of a systems biology application along with its graphics environment. Complex graphics based workflows, ubiquitous in systems biology, can now be easily exported and reproduced on many different platforms. GUIdock uses Docker, an open source project that provides a container with only the absolutely necessary software dependencies and configures a common X Windows (X11) graphic interface on Linux, Macintosh and Windows platforms. As proof of concept, we present a Docker package that contains a Bioconductor application written in R and C++ called networkBMA for gene network inference. Our package also includes Cytoscape, a java-based platform with a graphical user interface for visualizing and analyzing gene networks, and the CyNetworkBMA app, a Cytoscape app that allows the use of networkBMA via the user-friendly Cytoscape interface.

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“…It provides very powerful visualization tools to map a variety of categorical and numeric data into visual attributes associated with the nodes and edges of node-link diagrams. Unfortunately, Cytoscape does not provide any inherent animation capabilities, making it difficult to use interpolation to detect changes between two states, however, Cytoscape does provide a rich infrastructure for extending its core functionality through “apps” 3 . Several Cytoscape apps provide some animation capabilities.…”

Section: Introductionmentioning

confidence: 99%

CyAnimator: Simple Animations of Cytoscape Networks

et al. 2015

Self Cite

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CyAnimator (http://apps.cytoscape.org/apps/cyanimator) is a Cytoscape app that provides a tool for simple animations of Cytoscape networks. The tool allows you to take a series of snapshots (CyAnimator calls them frames) of Cytoscape networks. For example, the first frame might be of a network shown from a ”zoomed out” viewpoint and the second frame might focus on a specific group of nodes. Once these two frames are captured by the tool, it can animate between them by interpolating the changes in location, zoom, node color, node size, edge thickness, presence or absence of annotations, etc. The animations may be saved as a series of individual frames, animated GIFs, or H.264/MP4 movies.CyAnimator is available from within the Cytoscape App Manager or from the Cytoscape app store.

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The Cytoscape app article collection

Cited by 9 publications

References 5 publications

Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity

Global temporal dynamic landscape of pathogen-mediated subversion of Arabidopsis innate immunity

GUIdock: Using Docker Containers with a Common Graphics User Interface to Address the Reproducibility of Research

CyAnimator: Simple Animations of Cytoscape Networks

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