Welcome to the Stuart Lab Interaction Browser!

What is the Interaction Browser?

The Interaction Browser (IB) is a web application developed in Josh Stuart's Bioinformatics lab at UCSC. It is used to visualize and combine interaction data from a large number of datasets. The IB organizes the individual datasets into networks that can be switched on/off in the visualization of a biological network. The networks include datasets representing various types of data such as expression and protein interaction.

What do I need to use the Interaction Browser?

The Interaction Browser is designed to run in a web browser without the need to install any additional software. The Interaction Browser is primarily tested on the current version of Chrome and Firefox. Some web browser incompatibilities prevent the Interaction Browser from functioning properly on other browsers.

Tutorials for Displaying an Interaction Network

Looking for CircleMaps?

A typical heatmap visualizes data in a samples-by-genes grid. Each dataset is visualized in its own grid. A CircleMap visualizes the data on a per-gene basis. Each gene gets a CircleMap. The data row that represents the measurements for the gene is wrapped around the node. This is done for each dataset with each one producing a separate ring. Additionally, the sample ordering in each ring (even across CircleMaps) is maintained so that each "spoke" in the CircleMap represents one sample's data. CircleMaps in the Interaction Browser allow users to simultaneously view multiple datasets covering a common set of samples in an interactive network graph. To get started, check out the tutorial here.


The Stuart lab also offers a command-line tool for creating CircleMap images. The scripts for drawing CircleMap images are available at:


Sample Network

Here is a sample network to try out. This is the `Class I PI3K signaling events mediated by Akt' pathway from NCI-PID.


The Interaction Browser and CircleMaps are described in the 2013 Web Services issue of Nucleic Acids Research:
Wong CK, Vaske CJ, Ng S, Sanborn J, Benz S. Haussler D, Stuart J. The UCSC Interaction Browser: Multi-dimensional data views in pathway context. Nucleic Acids Research. 2013 Jul 1;41(Web Server issue):W218-24. doi: 10.1093/nar/gkt473. PMID:23748957.
CircleMaps are also described in the review article:
Schroeder MP, Gonzalez-Perez A, Lopez-Bigas N. Visualizing multidimensional cancer genomics data. Genome Med. 2013 Jan 31;5(1):9. doi:10.1186/gm413. PMID:23363777.
CircleMaps were used to visualize PARADIGM data in:
Vaske CJ, Benz SC, Sanborn JZ, Earl D, Szeto C, Zhu J, Haussler D, Stuart JM. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics. 2010 Jun 15;26(12):i237-45. doi: 10.1093/bioinformatics/btq182. PMID:20529912.

Let's go to the Interaction Browser!

This project was funded by an NSF CAREER award