Announcing Cerebral v.2.8.2- January, 2012
We are pleased to announce the release of Cerebral v.2.8.2! In this updated version of the program, compatible with the new Cytoscape 2.8.2 release (Update courtesy of Winston Haynes), we introduce our new multi-experiment comparison tool. With this new functionality, users can now upload, compare, contrast and cluster quantitative data from multiple experiments. Please try out the program and let us know what you think!
Cerebral (Cell Region-Based Rendering And Layout) is a Java plugin for the widely used open-source Cytoscape molecular interaction viewer. While Cytoscape offers a number of built-in graph layout options (e.g. spring-embedded, hierarchical, circular, organic...), all of these are based on mathematical and physical principles and do not take biological information into account. As a result, layouts do not resemble "traditional" signaling pathway/system diagrams, which typically show interacting proteins overlaid on an image of the cell - extracellular proteins and membrane receptors at the top, adapter proteins in the cytoplasm, and nuclear proteins and pathway-regulated genes at the bottom. Furthermore, while Cytoscape allows users to colour the nodes of a network according to any desired attribute, for example expression data from a microarray or other experiment, there is no function that permits the simultaneous comparison of multiple quantitative datasets.
Cerebral is a plugin that enhances Cytoscape's functionality by using extra annotation provided by the user to both automatically generate a more pathway-like representation of a network and to provide an environment for the visualization, comparison, and clustering of expression data from multiple conditions. Cerebral uses subcellular localization annotation to create a layered view of a cell, placing nodes in the region of the screen corresponding to the appropriate localization. Cerebral can also place a subset of nodes, regulated genes for example, at the bottom of the screen and can further group these bottommost nodes according to any user-specified attribute. Small multiple views enable a user to see expression data from 2 or more conditions overlaid on a network, while a difference view allows two conditions to be selected and a new view is coloured based on the changes between the selected conditions. An interactive k-means clustering tool also allows users to cluster their data, using a slider to adjust the number of desired clusters, and quickly select nodes based on cluster membership.
While Cerebral was designed with biological pathways in mind, it can also be used to lay out any graph that requires stratification
according to some characteristic and thus can be used by researchers in a variety of fields, including the social sciences.