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To display and/or sort additional data, you must return to the Columns and/or Sorting tabs to set display parameters, then re-run the search. The new search results will display the additional information, with the columns and data sorted as you specified. See https://wiki.nci.nih.gov/x/B4DnAg#3-SearchingacaIntegratorStudy-ResultsTypeTab. Results Type Tab.
caIntegrator paginates search results into pages of configurable size (default 20) with standard paginated navigation controls. To sort columns by ascending or descending parameters for on any displayed field, click on the underlined column header.
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 on page 63 #Exporting Data. See also .
Browsing Query Results
The query results that can display depend upon the criteria you established for the search. Follow the links below for more information about the category of data you searched.
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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 on page 60 Results Type Tab.
Gene Expression Data
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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For Gene criteria, the cells display the median gene expression value for each gene. By each gene symbol, caIntegrator displays an icon (
) which you can click to open the Cancer Genome Anatomy Project (CGAP) showing data for the gene, shown . An example shows in the following figure.
If you have selected Gene Expression on the Results Type tab, then the column headers are a clickable label which sorts the entire table on that column. If you selected Reporter ID on the Results Type tab, the Reporter ID is clickable (and the gene is not clickable).
For fold-change criteria, the cells display the normalized signal-based value for a given reporter for a given sample. In the results matrix, caIntegrator highlights matrix values for fold change results that meet fold change criteria. Red represents upregulated values and blue indicates downregulated values. The following two figures display gene name search results with gene reporter type display in the first and reporter ID reporter type display in the second. Note the left hand column in each example.
- Genomic data does not display in tandem with subject annotation and imaging data; it only displays when you select the Gene Expression result type on the Results Type tab. Genomic data is however, filtered by subject annotation and imaging query criteria configured on the Criteria tab.
- Click the Export Options CSV link to download the CSV file whose data displays on the Search Results tab. When you do so, the CSV file opens automatically in MS Excel or similar applications for working with spreadsheets, showing the columns and sorting as you defined them in caIntegrator on the appropriate tabs.
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*
If after defining copy number criteria on the Criteria tab and running a copy number query, (see on page 55 Copy Number Searches), 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.
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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, enter one or more gene symbols in the text box or click the icons to locate genes in the following databases. If you enter more than one gene in the text box, separate the entries by commas.
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, alt="The Edit Gene List for reviewing, editing the name or deleting a gene list. The Edit Subject List page is comparable."!
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When the image Study is in the checked boxes (regardless of image series being there or not), the system aggregates up to the Image Study level.
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This flowchart illustrates the relationship of patient to study to series and lastly to images.
For example, the Study Instance UID is the set of images resulting from one patient office visit. When you upload a spreadsheet of an image series, the hierarchy of images in an image series might look like this:
Study Instance UID (one office visit):
Brain (image series)
- Brain image 1
- Brain image 2
- Brain image 3
Leg (image series)
- Leg image 1
- Leg image 2
- Leg image 3
You can add details for images by configuring image annotations on the Results Type tab. Annotations listed there are the column headers in the image series CSV file(s) that were uploaded to the study. Examples of image details include the following:
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Exporting Data
search results:exporting data;exporting:dataYou 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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