: Getting Started

Visualizing genomic profile data in the context of known biological pathways

The enables researchers to visualize complex multi-dimensional genomic profiling data in the context of known biological pathways. This page provides a short tutorial for using the software and a webstart with sample data.

Getting Started

To launch the software, click the button below:

Sample Dataset

This will launch a Webstart version of Cytoscape, pre-loaded with all the necessary plugins, and a 91 sample dataset derived from the TCGA Glioblastoma Pilot Project. This dataset contains mutations, copy-number alterations, and expression data for 91 samples.

Once Cytoscape starts, you will see the following screen:

Cytoscape Screenshot with GBM pathway data loaded.

Browsing Genomic Profile Data in the Context of Biological Pathways

Once you have loaded pathway data, plus one or more genomic profiles, Cytoscape will automatically map the most recently loaded genomic profile data set to your pathway, and display it via a heat map. For example, the screenshot below displays mRNA expression data in the context of Glioblastoma pathway data:

Cytoscape Screenshot with GBM pathway data loaded.

To navigate through the genomic profiling and pathway data, please note the following:

Additional Options for Browsing Genomic Profile Data

The also enables you to explore specific types of scientific questions.

For example, you can focus in on one specific gene, and determine if expression profiles are correlated with copy number data. To do so, select "Constant:gene" from the "Constant:datatype" pull-down menu, and then then select a gene, e.g. "EGFR":

Gene Centric View.

Alternatively, you can focus in on one specific sample and again determine if expression profiles are correlated with copy number data. To do so, select "Constant:sample" from the "Constant:datatype" pull-down menu, and then then select a sample number, e.g. 10:

Sample Centric View.

In addition, you can view up to four data files simultaneously in the heatmap. To do so, load at least two data files, then hold down the shift key and press the F2 key. Continuing pressing the F2 key to return back to the single data file view.

Multiple Data File View.

Lastly, network nodes can be annotated with data file information. To do so, hold down the shift key and press the F3 key. Pressing the F3 key again will remove the data file annotations.

Multiple Data Type Nodes.

Tips

Additional Information

Additional information regarding the is available at the links below:

For general information regarding Cytoscape, please see the Cytoscape web site and user manual.