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Page History
...
Viewing
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Data
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with
...
the
...
Integrative
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Genomics
...
Viewer
...
Once
...
you
...
have
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run
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a
...
query
...
for
...
...
...
,
...
or
...
have
...
run
...
analyses
...
for
...
...
...
,
...
or
...
analyses
...
for
...
genomic
...
data,
...
you
...
can
...
view
...
results
...
in
...
the
...
Integrative
...
Genomics
...
Viewer
...
(IGV).
...
The
...
IGV
...
is
...
a
...
high-performance
...
visualization
...
tool
...
for
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interactive
...
exploration
...
of
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large,
...
integrated
...
datasets.
...
It
...
supports
...
a
...
wide
...
variety
...
of
...
data
...
types
...
including
...
sequence
...
alignments,
...
microarrays,
...
and
...
genomic
...
annotations.
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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.
Method 1 IGV
- With the appropriate study open, at the bottom of the Query Results page, click the View in Integrative Genomics Viewer button.
- If you click the button at the bottom of the page with any of the query results line items selected, caIntegrator creates IGV files, with a monitor informing you of this. After the files are created, click the Launch Integrative Viewer hypertext link.
- Follow the instructions through the intermediate dialog boxes. After clicking Open with the Java program listed, the
IGV.jnlpopens, displaying the dataset in the computer screen. An example displays in the following figure.
- Move your mouse to hover over the genes graphic at the bottom of the page, indicated in the figure.
- Click the mouse when you've identified a gene of interest.
This opens the genome site at UCSC, where you can learn more about the gene. The following figures exhibits the kind of metadata you can expect from the UCSC genome site.
Method 2 IGV
- With the appropriate study open, click Integrative Genomics Viewer on the left sidebar. This opens the View IGV Selector page, shown in the following figure.
- In the drop-down list, select the Gene Expression Platform for the data you want to view.
- Select the Copy Number Platform ID.
- The Annotations - Default panel displays existing annotation fields for the gene expression data in the open study. Select those fields you want to view when you open the IGV. Use the buttons for convenience if you want to Select All or Unselect All, when all are checked.
- Click View to see the data in the Integrative Genomic Viewer. caIntegrator creates IGV files of the data.
- After the files are created, click the Launch Integrative Viewer hypertext link that appears.
- Continue with Step 3 in Method 1 IGV.
Viewing Data with Heat Map Viewer
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).
| Info | ||
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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.
Method 1 HMV
- With the appropriate study open, at the bottom of the Query Results page, click the View in Heat Map Viewer button.
- If you click the button at the bottom of the page with any of the query results line items selected, caIntegrator creates HMV files, with a monitor informing you of this. After the files are created, click the Launch Heat Map Viewer hypertext link.
- Follow the instructions through the intermediate dialog boxes. After clicking Open with the Java program listed, the runs, displaying the dataset in the computer screen. An example displays in the following figure.
Method 2 HMV
- With the appropriate study open, click Heat Map Viewer on the left sidebar. This opens the View Heat Map Viewer Selector page, shown in the following figure.
- Select the appropriate Copy Number Platform in the drop down list.
- The Annotations - Default panel displays existing annotation fields for the gene expression data in the open study. Select one or more annotations in the annotation list. For convenience, you can use the Select All or Unselect All buttons.
- Click View to view the data you select in Heat Map Viewer. caIntegrator creates Heat Map Viewer files of the data.
- After the files are created, click the Launch Heat Map Viewer hypertext link that appears.
Continue with Step 3 in Method 1 HMV.
Info title HMV help files For interpretation of the results and using HMV features, see the help files opened from HMV.
Java for IGV and Heat Map Viewer
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
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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.
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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. {info:title=Note} For more information about the Integrative Genomics Viewer or to connect independently to the IGV home page, see [Integrative Genomics Viewer login|http://www.broadinstitute.org/igv/log-in.] {multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}. You may also want to refer to the [IGV User Guide|http://www.broadinstitute.org/software/igv/UserGuide] {multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}. 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 Viewewr].{info} There are two ways to integrate caIntegrator with the IGV. To configure the connection to IGV, follow one of these methods. h6. _Method 1 IGV_ # With the appropriate study open, at the bottom of the Query Results page, click the *View in Integrative Genomics Viewer* button. # If you click the button at the bottom of the page with any of the query results line items selected, caIntegrator creates IGV files, with a monitor informing you of this. After the files are created, click the *Launch Integrative Viewer* hypertext link. # Follow the instructions through the intermediate dialog boxes. After clicking *Open* with the Java program listed, the {{IGV.jnlp}} opens, displaying the dataset in the computer screen. An example displays in the following figure. !IGV session80.png|vspace=4, alt=”IGV Viewer displaying expression results from data isolated in caIntegrator”! # Move your mouse to hover over the genes graphic at the bottom of the page, indicated in the figure. # Click the mouse when you've identified a gene of interest. This opens the genome site at UCSC, where you can learn more about the gene. The following figures exhibits the kind of metadata you can expect from the UCSC genome site. !GABRG1 at UCSC80.png|vspace=4, alt=”Example of the kind of metadata you can learn about a gene at the UCSC genome website”! h6. _Method 2 IGV_ # With the appropriate study open, click *Integrative Genomics Viewer* on the left sidebar. This opens the View IGV Selector page, shown in the following figure. !IGV selector80.png|vspace=4, border=1, alt=”The page for configuring the connection to the IGV”! # In the drop-down list, select the *Gene Expression Platform* for the data you want to view. # Select the *Copy Number Platform* ID. # The Annotations - Default panel displays existing annotation fields for the gene expression data in the open study. Select those fields you want to view when you open the IGV. Use the buttons for convenience if you want to *Select All* or *Unselect All{*}, when all are checked. # Click *View* to see the data in the Integrative Genomic Viewer. caIntegrator creates IGV files of the data. # After the files are created, click the *Launch Integrative Viewer* hypertext link that appears. # Continue with Step 3 in [#Method 1 IGV]. h3. Viewing Data with Heat Map Viewer Once you have run a query for [gene expression|caIntegrator:4 - Searching a caIntegrator Study#GeneExpressionSearches], or for [copy number|caIntegrator:4 - Searching a caIntegrator Study#CopyNumberSearches], or have run analyses on genomic data, you can view results in the Heat Map Viewer (HMV). {info:title=Note} For more information about the Heat Map Viewer or to connect independently to the HMV home page, see [Heat Map Viewer documentation|https://cgwb.nci.nih.gov/cgi-bin/heatmap]. For HMV documentation, see [https://cgwb.nci.nih.gov/goldenPath/heatmap/documentation/index.html]. 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.].{info} There are two ways to integrate caIntegrator with the Heat Map Viewer. To configure the connection, follow one of these methods. h6. _Method 1 HMV_ # With the appropriate study open, at the bottom of the Query Results page, click the *View in Heat Map Viewer* button. # If you click the button at the bottom of the page with any of the query results line items selected, caIntegrator creates HMV files, with a monitor informing you of this. After the files are created, click the *Launch Heat Map Viewer* hypertext link. # Follow the instructions through the intermediate dialog boxes. After clicking *Open* with the Java program listed, the runs, displaying the dataset in the computer screen. An example displays in the following figure. !heat map viewer results280.png|vspace=4, alt=”Data display in Heat Map Viewer”! h6. _Method 2 HMV_ # With the appropriate study open, click *Heat Map Viewer* on the left sidebar. This opens the View Heat Map Viewer Selector page, shown in the following figure. !view heat map selector80.png|vspace=4, border=1, alt=”View Heat Map Selector page”! # Select the appropriate *Copy Number Platform* in the drop down list. # The Annotations - Default panel displays existing annotation fields for the gene expression data in the open study. Select one or more annotations in the annotation list. For convenience, you can use the *Select All* or *Unselect All buttons{*}. # Click *View* to view the data you select in Heat Map Viewer. caIntegrator creates Heat Map Viewer files of the data. # After the files are created, click the *Launch Heat Map Viewer* hypertext link that appears. # Continue with Step 3 in [#Method 1 HMV]. {info:title=Note} For interpretation of the results and using HMV features, see the help files opened from HMV.{info} h4. Java for IGV and Heat Map Viewer 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. For more information, see [http://www.java.com/en/download/faq/java_webstart.xml] {multi-excerpt-include:wikicontent:Exit Disclaimer to Include|name=ExitDisclaimer|nopanel=true}. 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. {info:title=Note} 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.{info} |
