Google Play icon

Cytoscape: a growing app network for network biology

Share
Posted October 22, 2014

Collating and visualizing vast network data can be as easy as downloading an app – an open source software platform, Cytoscape, offers a range of programs to view and integrate manipulate complex data, or create a custom app for your needs. The platform is host to a variety of data visualization apps which are handy from visualizing metabolic networks to gathering social interactions from the web.

Human interactome (the set of all protein-to-protein interactions) visualized in Cytoscape 2.6. Credit: Andrew Garrow via Flickr (CC BY-NC-ND 2.0)

Human interactome (the set of all protein-to-protein interactions) visualized in Cytoscape 2.6. Credit: Andrew Garrow via Flickr (CC BY-NC-ND 2.0)

The platform is flexible enough to allow data visualization in a variety of disciplines, but Cytoscape is most commonly used to manipulate molecular networks and biological pathways, and is an important tool in systems biology.

One of the largest collaborative initiatives dedicated to biological pathways – Wikipathways, has recently been linked to Cytoscape, allowing custom visualization and computational analyses for an enhanced research experience. A recent article published in F1000Research explores how collaborative Wikipathways data can be exported and visualized within the Wikipathways App.

The tool now allows network data to be easily queried and imported from the Wikipathways web service, and the pathways of interest can then displayed in one of the two ways. One is an annotated pathway, containing full biological information associated with each element. Alternatively, the data can be visualized as a simple network, representing the relationships of different members (e.g. molecules).

Cardiac Hypertrophic Response pathway 01

The Cardiac Hypertrophic Response pathway loaded within WikiPathways App as an annotated pathway (above) and as a simple network after topological analysis (below). Images courtesy of the researchers.

The Cardiac Hypertrophic Response pathway loaded within WikiPathways App as an annotated pathway (above) and as a simple network after topological analysis (below). Images courtesy of the researchers.

The latter feature allows users to merge pathways, visualize networks in different layouts or extend the pathway. Moreover, the topology of the network can be analyzed computationally, such as with a built-in Cytoscape’s NetworkAnalyzer tool. Other apps within the platform can be used to edit or add data to the network, or identify trends of interest (these include CyTargetLinker, clusterMaker2, jActiveModules).

According to the authors, Wikipathways App plays an important part in making complex network data analysis more convenient to researchers, and could be used to study a range of pathways, from the smallest atomic interactions in proteins to networks of cells, organisms or whole populations.

Over two hundred other freely available apps for network analysis can be found in Cytoscape App Store.

An F1000Research article collection dedicated to the ever-growing network of Cytoscape apps and tips for developers can be accessed here.

Source: Kutmon M, Lotia S, Evelo CT and Pico AR. WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization [v2; ref status: indexed, https://f1000r.es/49lF1000Research 2014, 3:152 (doi: 10.12688/f1000research.4254.2)

Written by Eglė Marija Ramanauskaitė

Featured news from related categories:

Technology Org App
Google Play icon
86,012 science & technology articles

Most Popular Articles

  1. Universe is a Sphere and Not Flat After All According to a New Research (November 7, 2019)
  2. NASA Scientists Confirm Water Vapor on Europa (November 19, 2019)
  3. How Do We Colonize Ceres? (November 21, 2019)
  4. This Artificial Leaf Turns Atmospheric Carbon Dioxide Into Fuel (November 8, 2019)
  5. Scientists created a wireless battery free computer input device (December 1, 2019)

Follow us

Facebook   Twitter   Pinterest   Tumblr   RSS   Newsletter via Email