Category Cross-Omics>Pathway Analysis/Tools

Abstract GenePro is a Cytoscape (see G6G Abstract Number 20092) plug-in for the visualization and analysis of protein and gene interaction networks at multiple levels of resolution.

At low resolution, GenePro displays individual clusters of proteins or genes as nodes, and the relationships between them as edges.

Each node can optionally be colored as a pie graph, illustrating the distribution of that cluster's members within a second network.

This greatly facilitates the validation of functional modules - by allowing visual comparisons to known modules - and the analysis of cluster characteristics such as biological function, cellular localization, or evolutionary conservation.

At high resolution, the cluster members and their mutual interactions are displayed for more detailed analysis.

GenePro furthermore offers various options of mapping conditions dependent 'mRNA expression levels' onto protein interactions networks and networks of complexes.

Visualizing Clusters of Interacting Proteins --

GenePro makes this possible by using composite nodes (as stated above) that represent groups of genes/proteins onto which a set of properties of interest can be mapped, and then visualized or queried interactively.

Furthermore, the composite nodes within these graphs are connected to one another on the basis of a derived metric which contains relevant information about the strength of the link between nodes.

The clusters/nodes are linked to one another whenever there are at least two observed interactions between proteins in each cluster, with the thickness of the edge being proportional to the number of such interactions.

This representation positions the protein clusters (or complexes) in the global interaction network, revealing which of the clusters is highly connected to other clusters and suggesting the extent to which the predicted complexes may share members in vivo.

Some clustering procedures produce clusters that share components (overlapping clusters). For such cases the user can specify edges between nodes to represent the number of shared proteins.

To facilitate the validation and analysis of the computed clusters, GenePro offers an additional set of features.

It lets you view each node, representing a cluster of proteins, as a pie chart (as stated above) where the size and color of the wedges represent the fraction of the proteins in the cluster that share the same property.

Positioning the mouse over a given wedge displays the number and names of the proteins that belong to a given complex within the cluster, and a mouse click over the same wedge highlights proteins in other nodes anywhere in the network that belong to the same complex.

This latter feature provides an overview of the extent to which proteins from the same complex are distributed throughout other clusters.

These visualization features are very general and can be used to map any two groupings of proteins onto one another.

In addition to complexes/clusters, such groupings may include

(1) functional categories,

(2) sub-cellular localizations,

(3) level of sequence conservation and

(4) groups of co-regulated genes/proteins.

And all these can be mapped onto the network of complexes/clusters and vice versa.

Additional options for mapping mRNA expression data onto an individual gene in the network of protein/gene clusters are also available, as are various options for interactively querying the displayed information.

Visualizing Individual Clusters in the Context of the Interaction Network -- In addition to displaying and querying networks of protein clusters, GenePro allows analyzing the proteins in individual clusters and their pairwise interactions.

A double-click on a given cluster displays a sub-graph, whose nodes are the proteins within the cluster (red nodes), as well as their nearest neighbors from other clusters (blue nodes) and the arcs are their interactions in the protein–protein interaction (PPI) network.

Clicking on an arc between two genes displays a table listing the reliability score of the interaction, as well as the raw score of each observation recorded for the interaction in the original proteomics experiments.

System Requirements

Cytoscape and JRE 1.5+


GenePro is produced in association with these institutions.

Manufacturer Web Site GenePro

Price Contact manufacturer.

G6G Abstract Number 20305

G6G Manufacturer Number 102610