|echo $app_name; ?>: Getting Started|
Visualizing genomic profile data in the context of known biological pathways
The echo $app_shortname; ?> 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.
To launch the software, click the button below:
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:
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:
To navigate through the genomic profiling and pathway data, please note the following:
- By default, individual samples are displayed along columns, and the first sample is mapped to the current pathway (noted by the green rectangle in the screenshot above). To switch samples, select any of the left/right column buttons, or select an individual field within the heat map. This will automatically swap the entire genomic profile for the selected sample and display it on the current pathway.
- By default, individual genes within the network are displayed along rows. If you select one of the row navigation buttons, e.g. Next Row, the pathway view will automatically center on the newly selected gene.
- By default, the most recently loaded data file is mapped to the pathway. To swap to copy number data, select "Copy Number Data" from the pull-down menu located directly to the right of "Constant: datatype".
Additional Options for Browsing Genomic Profile Data
The echo $app_shortname; ?> 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":
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:
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.
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.
- To resize all the columns within the heat map, hold down the shift key and click and drag a column edge.
- To export the heatmap as a Portable Document Format File (PDF), hold down the shift key and press the F1 key.
- To view multiple data files simultaneously, hold down the shift key and press the F2 key. Continuing pressing the F2 key to return back to the single data file view.
- To annotated network nodes with data file information, hold down the shift key and press the F3 key. Pressing the F3 key again will remove the data file annotations.
Additional information regarding the echo $app_shortname; ?> is available at the links below:
- Configuration options: includes details regarding configuration of the color gradient and heat map.
- File format: includes details regarding the file format of genomic profile data.
- Retrieving Pathways: describes how to retrieve pathways from Pathway Commons, and overlay genomic profile data onto known pathways and interaction networks.
- Loading, Unloading, & Saving Genomic Data: includes details regarding the various ways to load & unload genomic profile data.