R2 and Cytoscape: Graph based integration and analysis of molecular biological data

Piet Molenaar

Academic Medical Center, University of Amsterdam, the Netherlands

Cytoscape provides a convenient way of annotating your network of choice with micro array data through an id-mapping mechanism provided by the BioMartPlugin. In this demo I’ll show an example of that.

Probeset validation and statistical analysis however, are lacking from this type of analysis workflow. Driven by questions from molecular biologists we therefore set out to develop R2, a web-based array data analysis platform (humangenetics-amc.nl). Through a webstart based integration with Cytoscape, the results of this data analysis can be visualized as a network.

This provides access to a wealth of plugins to further functionally enrich your network and derive new biologically testable hypotheses. In that context I will demo the Gene Ontology plugin BiNGO, the cluster detection tool MCODE and the network inferring tool CytoProphet. They will be used for analysis of our timeseries experiments where the response to gene-silencing through siRna was measured in Neuroblastoma cell-lines. Focus will be on the transcription factor backbone network.

Data keywords: Gene expression, Transcription factors, Probeset validation, Time series

Cytoscape keywords: Network and Attribute I/O, Network Inference, Functional Enrichment