Once you have run a query for gene expression, or have run analyses for copy number, or analyses for genomic data, you can view results in the Integrative Genomics Viewer (IGV).
The IGV is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types including sequence alignments, microarrays, and genomic annotations.
For more information about the Integrative Genomics Viewer or to connect independently to the IGV home page, see Integrative Genomics Viewer . You may also want to refer to the IGV User Guide . The IGV viewer and the NCI Heat Map viewer both require you to install a version of Java containing Java Web Start. For more information, see Java for IGV and Heat Map Viewer. |
There are two ways to integrate caIntegrator with the IGV. To configure the connection to IGV, follow one of these methods.
IGV.jnlp
opens, displaying the dataset in the computer screen. An example displays in the following figure.Once you have run a query for gene expression, or for copy number, or have run analyses on genomic data, you can view results in the Heat Map Viewer (HMV).
For more information about the Heat Map Viewer or to connect independently to the HMV home page, see Heat Map Viewer documentation or HMV documentation. The IGV viewer and the NCI Heat Map viewer both require you to install a version of Java containing Java Web Start. For more information, see Java for IGV and Heat Map Viewer.. |
There are two ways to integrate caIntegrator with the Heat Map Viewer. To configure the connection, follow one of these methods.
Continue with Step 3 in Method 1 HMV.
For interpretation of the results and using HMV features, see the help files opened from HMV. |
To use the IGV and the NCI Heat Map viewer, described in Viewing Data with the Integrative Genomics Viewer and Viewing Data with Heat Map Viewer, you must install a version of Java containing Java Web Start. You must install recent versions of the Java Development Kit (JDK 1.5.0 aka JDK 5.0 or newer) or Java Runtime Environment (JRE 1.5.0 aka JRE 5.0 or newer). The easiest option is to install JRE 5.0
Without Java Web Start, when you click Launch Integrative Genomics Viewer or Launch Heat Map Viewer, a dialog box displays in your browser giving you the option to save or open with igv.jnlp
(IGV) or retrieveFile.jnlp
(HMV). Clicking the Open option starts the Java Web Start Launcher (default), installing the Java app so that you can view the files.
The first time you launch the IGV or HMV with Java properly installed, regardless of browser type, a warning may appear: the "the digital signature cannot be verified". Click Run to proceed with opening the viewer. |