Cytoscape is a bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. Additional features are available as plugins. Plugins are available for network and molecular profiling analyses, new layouts, additional file format support and connection with databases. Plugins may be developed using the Cytoscape open Java software architecture by anyone and plugin community development is encouraged.
NetBox is a Java-based software tool for performing network analysis on human interaction networks. It is pre-loaded with a Human Interaction Network (HIN) derived from four literature curated data sources, including the Human Protein Reference Database (HPRD), Reactome, NCI-Nature Pathway Interaction (PID) Database, and the MSKCC Cancer Cell Map.
Currently, NetBox provides the analyzeNet.py method that is fully described in the manuscript: Automated Network Analysis Identifies Core Pathways in Glioblastoma (Currently in Review). This provides a simple command line interface for connecting genes into a network, identifying statistically significant "linker" genes, partitioning the network into modules, and executing two random background models. Results are then made available to the end user as an HTML web page and a series of network and attribute files, which can be loaded into Cytoscape for visualization and further analysis.
miRanda is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. MiRanda was developed at the Computational Biology Center of Memorial Sloan-Kettering Cancer Center. This software will be further developed under the open source model, coordinated by Anton Enright and Chris Sander ( ).
Although hundreds of miRNAs have been discovered, the functions of these miRNAs are not known. This viewer allows access to the predicted protein coding gene targets. Searching by miRNA will display a ranked list of gene targets and allow you to analyze each conserved target gene/sites in detail. Similarly, searching by gene name/identifier will display the sequence of the three prime UTR and the positions of the miRNA sites along the sequence, allowing you to analyze the target sites in detail.
Download the latest list of microRNA target genes and microRNA target sites.