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This chapter describes search results that caIntegrator returns after queries.
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Query Results Overview
After you launch a search of a caIntegrator study, the system automatically opens the Query Results tab showing the results of your search. If you have not configured the column and sort display parameters before launching the search, by default the tab shows only the subject identifiers and a column that allows you to select each row of the data subset.
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You can download search results as a CSV file. The file contains the annotations, columns and data sort configurations you specified in the search query. See #Exporting Data.
See #Subject Annotation and Imaging Data, #Gene Expression Data, and #Expanding Imaging Data Results.
Subject Annotation and Imaging Data Results
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If you run the search before configuring column and sort display parameters, only the \[subject\] ID that meet the criteria and a column allowing you to select each row appear on the table, as shown in the following figure. !imaging subj ID only75.png|vspace=4, alt="Query Results page"! |
You can add details for one or more subjects by configuring them on the Results Type tab. Annotations listed there are the column headers in the CSV file(s) that were uploaded to the study. For information about using the Results Type tab, see Results Type Tab.
Gene Expression Data Results
If after defining gene expression criteria on the Criteria tab, you select the Gene Expression result type on the Results Type tab, genomic data search results display in a gene expression data matrix. Because the data was downloaded from caArray, the data permissions granted there still apply. In other words, if you have been given access to the data in caArray, you can see it in caIntegrator.
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You can save genes identified in the search results as a gene list. For more information, see #Creating a Gene or Subject List.
Copy Number Data Results
After defining copy number criteria on the Criteria tab and running a copy number query, you should select the Copy Number result type on the Results Type Tab, and rerun the query. Copy number data search results display in a data matrix containing samples vs. genomic regions.
- Gene symbols display parallel to chromosome regions on the matrix.
- Sample ID column headings display the Subject ID/Sample ID (for example, E09262/E09262) because each calculation is based on a comparison of a tumor and matched blood sample from the same subject.
- The values in the Sample ID columns are mean segment values as calculated by the DNAcopy algorithm, shown in the following figure. These are expressed as log2 (test/reference, as in tumor/normal). For more information about the algorithm, see Bioconductor.
DNAcopy ouput values can be negative. If the test and the reference genomic samples both have two copies of a chromosomal region, the ratio of test/reference is '1', and the log2(1) = 0. That is, if there is no change in the chromosomal structure, then the value is 0. If there are more copies in the test sample (amplification of the chromosomal segment), the ratio of test to reference is greater than 1, and the log2(test/reference) is greater than 0. For example, if the test sample has 6, the ratio or test/reference is 6/2 = 3; log2(3) = 1.58. In a deletion, the test is less than the reference, for example 1. The DNAcopy output value would be log2(1/2) = log2(0.5) = -1.0. Values below -0.6 are often considered a deletion.
Creating a Gene or Subject List
From any page in caIntegrator that shows such a group, you can save a list of genes or subjects so you can use it for searches or analyses. This functionality can also be used where a gene or subject list was created outside of caIntegrator, for example, a list of subjects with validated mutation such as from TCGA projects, or a list of subjects with high EGFR expression or any lists of subjects with genomic or clinical characteristics determined with other tools.
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- Click the Create New List link in the left sidebar. This opens the Manage List page, shown in the following figure.
- Enter a name for the gene or subject list.
- Enter a description (optional).
- Select Make Visible to Others if you want the list to be visible to anyone who views the study. This selection places the list in the Global List folder in the left sidebar under Saved Lists. In any box where you can select lists, the term 'Global' will identify any list so identified when the list is created.
- Select the List Type, Subject or Gene.
- If you select Subject, enter the Subject IDs in the text box that appears. Proceed with step 7.
- If you select Gene, proceed with step 6.
- For Gene Symbol, caIntegrator provides three methods whereby you can obtain gene symbols for creating a gene list. For more information, see #Choosing Genes.
- If you so choose, you can upload a gene or subject ID list. For the Upload File field, click the Browse button to navigate to a .csv file made up of gene symbols. caIntegrator converts the comma-separated content to a gene list.
Wiki Markup Click *Create List* at the bottom of the page. caIntegrator now opens the Edit \[Subject or Gene\] List page which shows the name and symbols of the newest gene list, shown in the following figure. !edit gene list80.png|vspace=4, border=1, alt="The Edit Gene List for reviewing, editing the name or deleting a gene list. The Edit Subject List page is comparable."!
See #Editing a Gene or Subject List for information about the edit feature.
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When you perform a GISTIC analysis, caIntegrator automatically saves the retrieved genes in the Saved Copy Number analysis in the left sidebar. For a query or plot analysis, they also appear in the Gene Picker dialog box described in #Choosing Genes. |
Editing a Gene or Subject List
To view a gene list or subject list in caIntegrator, under Study Data in the left sidebar, click Saved Lists > Global Lists, or My Lists. Select the list/analysis you want to open. The system displays gene or subject lists that have been saved for the open study.
You can initiate the following functions on this page:
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Imaging Data Results
In reviewing imaging search results, it is important to understand the hierarchy of submissions in NBIA. For more information, see #Relationship of Subject to Study to Series to Images.
If you run a search before configuring column and sort display parameters, only the Subject Identifiers for the patients/images that meet the criteria and a column containing one check box per row display by default. An example displays in the following figure.
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You can set display parameters for the results on the Columns and Sorting tabs. For more information, see #Results Type Tab.
See also #caIntegrator and NBIA, [#Retrieving DICOM Images and #Example of Retrieving Images.
caIntegrator and NBIA
Images can be accessed in NBIA if you see buttons on the Search Results page. See the Imaging Note in #Results Type Tab. You can click links on the Search Results tab to view or download image data.
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- Forward to NBIA – This button is linked to results you have selected by row. Click the button to open NBIA, where the image series you select are loaded in the NBIA image basket. In the event that the caIntegrator study was NOT configured with image annotation for an image series, caIntegrator sends NBIA a list of Study Instance UIDs, for which NBIA will add all corresponding image series to the basket. In the event that the caIntegrator study was configured with annotations for an image series, the system sends NBIA a list of Image Series IDs, for which NBIA adds all corresponding image series to the basket.
Retrieving DICOM Images
On the caIntegrator imaging data Search Results page, you can click the Retrieve DICOM Images button which is linked to results you have selected by row. caIntegrator retrieves the corresponding image(s) from NBIA through the grid. NBIA organizes the download file by patient ID, StudyInstance UID, and ImageSeries UID, and compresses it into a zip file. When caIntegrator notifies you that the file is retrieved, the DICOM Retrieval page indicates whether the retrieved files are Study Instance UIDs or Image Series UIDs, shown in the following figure.
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To best understand this, it is important to review the hierarchy of submissions in NBIA. For more information, see #Relationship of Subject to Study to Series to Images.
Example of Retrieving Images
If you are searching a study that has image data and image annotation(s) for at least one image series, you would follow these steps:
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Exporting Data
You can choose to download tabular search results as a CSV file. Click the Export .csv link at the bottom of the page. You may need to scroll the page to see it. The file contains the annotations, columns and data sort configurations you specified in the search query.
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