Mosaic: making biological sense of complex networks by Chao Zhang, Kristina Hanspers, Allan Kuchinsky, Nathan Salomonis, Dong Xu, and Alexander R. Pico. (Bioinformatics (2012) 28 (14): 1943-1944. doi: 10.1093/bioinformatics/bts278)
Abstract:
We present a Cytoscape plugin called Mosaic to support interactive network annotation, partitioning, layout and coloring based on gene ontology or other relevant annotations.
From the Introduction:
The increasing throughput and quality of molecular measurements in the domains of genomics, proteomics and metabolomics continue to fuel the understanding of biological processes. Collected per molecule, the scope of these data extends to physical, genetic and biochemical interactions that in turn comprise extensive networks. There are software tools available to visualize and analyze data-derived biological networks (Smoot et al., 2011). One challenge faced by these tools is how to make sense of such networks often represented as massive ‘hairballs’. Many network analysis algorithms filter or partition networks based on topological features, optionally weighted by orthogonal node or edge data (Bader and Hogue, 2003; Royer et al., 2008). Another approach is to mathematically model networks and rely on their statistical properties to make associations with other networks, phenotypes and drug effects, sidestepping the issue of making sense of the network itself altogether (Machado et al., 2011). Acknowledging that there is still great value in engaging the minds of researchers in exploratory data analysis at the level of networks (Kelder et al., 2010), we have produced a Cytoscape plugin called Mosaic to support interactive network annotation and visualization that includes partitioning, layout and coloring based on biologically relevant ontologies (Fig. 1). Mosaic shows slices of a given network in the visual language of biological pathways, which are familiar to any biologist and are ideal frameworks for integrating knowledge.
[Fig. 1 omitted}
Cytoscape is a free and open source network visualization platform that actively supports independent plugin development (Smoot et al., 2011). For annotation, Mosaic relies primarily on the full gene ontology (GO) or simplified ‘slim’ versions (http://www.geneontology.org/GO.slims.shtml). The cellular layout of partitioned subnetworks strictly depends on the cellular component branch of GO, but the other two functions, partitioning and coloring, can be driven by any annotation associated with a major gene or protein identifier system.
You will need:
- Cytoscape installed. +
- Mosaic.jar +
- CyThesaurus.jar
As per the Mosaic project page.
The Mosaic page offers additional documentation, which will take a while to process. I am particularly interested in annotations of the network driving partitioning.