Cytoscape.js: a graph theory library for visualisation and analysis

Franz, Max; Lopes, Christian; Huck, Gerardo; Dong, Yue; Sumer, Onur; Bader, Gary D.

doi:10.1093/bioinformatics/btv557

Cited by 565 publications

(431 citation statements)

References 7 publications

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“…The deployment of co-expression networks onto our web resource was performed through the use of Cytoscape.js JavaScript library (23) (https://github.com/cytoscape/cyjs-sample/wiki). …”

Section: Methodsmentioning

confidence: 99%

Atlas ofSchistosoma mansonilong non-coding RNAs and their expression correlation to protein-coding genes

et al. 2018

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Long non-coding RNAs (lncRNAs) have been widely discovered in several organisms with the help of high-throughput RNA sequencing. LncRNAs are over 200 nt-long transcripts that do not have protein-coding (PC) potential, having been reported in model organisms to act mainly on the overall control of PC gene expression. Little is known about the functionality of lncRNAs in evolutionarily ancient non-model metazoan organisms, like Schistosoma mansoni, the parasite that causes schistosomiasis, one of the most prevalent infectious-parasitic diseases worldwide. In a recent transcriptomics effort, we identified thousands of S. mansoni lncRNAs predicted to be functional along the course of parasite development. Here, we present an online catalog of each of the S. mansoni lncRNAs whose expression is correlated to PC genes along the parasite life-cycle, which can be conveniently browsed and downloaded through a new web resource http://verjolab.usp.br. We also provide access now to navigation on the co-expression networks disclosed in our previous publication, where we correlated mRNAs and lncRNAs transcriptional patterns across five life-cycle stages/forms, pinpointing biological processes where lncRNAs might act upon.Database URL: http://verjolab.usp.br

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“…The deployment of co-expression networks onto our web resource was performed through the use of Cytoscape.js JavaScript library (23) (https://github.com/cytoscape/cyjs-sample/wiki). …”

Section: Methodsmentioning

confidence: 99%

Atlas ofSchistosoma mansonilong non-coding RNAs and their expression correlation to protein-coding genes

et al. 2018

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“…It runs on most modern web browsers, without requiring any installations. PathwayMapper is based on the Cytoscape.js (Franz et al, 2016) graph library, uses backbone.js in the frontend, and node.js and the Google Realtime API in the backend. Through advanced customization of Cytoscape.js and newly developed extensions for this library, PathwayMapper is not only a state-of-the-art viewer supporting compound structures for complexes, families, processes, and cellular locations, but also an easy to use editor, due to tools such as automatic layout, node alignment, undo support, an overview window and real time collaborative editing support (Fig.…”

Section: Methodsmentioning

confidence: 99%

PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data

Bahceci

Doğrusöz

et al. 2017

Bioinformatics

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Motivation: While existing network visualization tools enable the exploration of cancer genomics data, most biologists prefer simplified, curated pathway diagrams, such as those featured in many manuscripts from The Cancer Genome Atlas (TCGA). These pathway diagrams typically summarize how a pathway is altered in individual cancer types, including alteration frequencies for each gene. Results: To address this need, we developed the web-based tool PathwayMapper, which runs in most common web browsers. It can be used for viewing pre-curated cancer pathways, or as a graphical editor for creating new pathways, with the ability to overlay genomic alteration data from cBioPortal. In addition, a collaborative mode is available that allows scientists to co-operate interactively on constructing pathways, with support for concurrent modifications and built-in conflict resolution. Availability and Implementation: The PathwayMapper tool is accessible at http://pathwaymapper. org and the code is available on Github (https://github.com/iVis-at-Bilkent/pathway-mapper).

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“…The web interface is implemented in JavaScript and runs on a NodeJS web server hosted on Amazon Web Services. The frontend interface uses Bootstrap framework for web design and CytoscapeJS (16) for network visualization.…”

Section: The Xtalkdb Websitementioning

confidence: 99%

XTalkDB: a database of signaling pathway crosstalk

et al. 2016

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Analysis of signaling pathways and their crosstalk is a cornerstone of systems biology. Thousands of papers have been published on these topics. Surprisingly, there is no database that carefully and explicitly documents crosstalk between specific pairs of signaling pathways. We have developed XTalkDB (http://www.xtalkdb.org) to fill this very important gap. XTalkDB contains curated information for 650 pairs of pathways from over 1600 publications. In addition, the database reports the molecular components (e.g. proteins, hormones, microRNAs) that mediate crosstalk between a pair of pathways and the species and tissue in which the crosstalk was observed. The XTalkDB website provides an easy-to-use interface for scientists to browse crosstalk information by querying one or more pathways or molecules of interest.

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Cytoscape.js: a graph theory library for visualisation and analysis

Cited by 565 publications

References 7 publications

Atlas ofSchistosoma mansonilong non-coding RNAs and their expression correlation to protein-coding genes

Atlas ofSchistosoma mansonilong non-coding RNAs and their expression correlation to protein-coding genes

PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data

XTalkDB: a database of signaling pathway crosstalk

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