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This section includes the following topics.

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AnchorRTF37303231343a204368617074RTF37303231343a204368617074Viewing Query Results
This chaptersection chapter describes search results that caIntegrator returns after queries.

Topics in this chaptersection include the following:

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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.
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 on page 60.
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.
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.

Subject Annotation and Imaging Data

If 

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search results:overviewAfter 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.
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 on page 60.
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.
See also .
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search results:browsingThe 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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<ac:structured-macro ac:name="anchor" ac:schema-version="1" ac:macro-id="52f175c2-ba0f-45c1-82e5-5d556cc7e31d"><ac:parameter ac:name="">RTF38333435343a204865616469</ac:parameter></ac:structured-macro>Subject Annotation and Imaging Data
search results:annotation data;search results:imaging dataIf 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 (). . !worddav18596fd9e615cb72d87b2e22d10863d6.png|height=324,width=561!

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• RTF38383730353a204361707469Query 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. AnchorRTF36313637343a204865616469RTF36313637343a204865616469

Gene Expression Data

search results:specifying gene expression dataIf 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.
You can select on the Results Type tab a preferred orientation for displaying the results: genes in rows and subjects in columns, or genes in columns and subjects in rows.
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 ().

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  Gene Name search 6 genes, Reporter Type: Reporter ID. Genes display in rows and subjects appear in columns.
• 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 .

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Copy Number Data*

search results:copy number data;copy number:search resultsIf after defining copy number criteria on the Criteria tab and running a copy number query, (see on page 55), you should select the Copy Number result type on the , 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 (). These are expressed as log2(test/reference, as in tumor/normal). For more information about the algorithm, see Replace this screen shot.

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  Data matrix displaying copy number search results

  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.

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Creating a Gene or Subject List

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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.
To create a list, follow these steps:

• Click the Create New List link in the left sidebar. This opens the Manage List page ():

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  Manage Gene List page
• Enter a name for the gene or subject list.
• Enter a description (optional).
• gene list:global;gene list:visibilitySelect 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.

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See Editing a List for information about the edit feature.

• GISTIC:saved genesWhen 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 .

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Choosing Genes

choosing genescaIntegrator caIntegrator provides three methods whereby you can obtain gene names for a gene expression search.

• caBIO:genes search;searching:caBIOcaBIO – This link searches caBIO, then pulls identified genes into caIntegrator for analysis.
• Click the caBIO icon ( ).
• Enter Search Terms. Note that caIntegrator can perform a search on a partial HUGO symbol. For example, as search using ACH would find matches with 'achalasia' and 'arachidonate'.
• Select if you want to search in Gene Keywords, Gene Symbols, Gene Alias, Database Cross Reference Identifier or Pathways (from the drop-down list).
• Gene Keywords searches the description field in caBIO; the result displays in the Full Name Column.
• Gene Symbols searches only the Unigene and HUGO gene symbols in caBIO.
• Gene Alias searches for one or more gene symbols which are synonymous for the current gene symbol.  
• Database Cross Reference Identifier searches for the symbol for this gene as it appears in other databases.
• Pathways searches only the pathway names in caBIO. Note that searching in Pathways is a two step process. First, the initial Pathway search produces search results which are pathways. Second, from the pathway search results screen, you must select pathways of interest, then click Search Pathways for Genes to obtain a list of genes related to the selected pathways.
• Select the Any or All choice to determine how your search terms will be matched. Any finds any match for any search term you entered. All finds only results that match all of the search terms.
• Choose the Taxon from the drop-down list and click Search. The search results display ().

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  Example caBIO gene search criteria and search results
• In the search results, use the check boxes to identify the genes whose symbols you want to use in the gene expression analysis.
• Click Use Genes at the bottom of the page. This pulls the checked genes into the Criteria tab ().

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  Genes pulled in from caBIO display on the Criteria tab
• Gene List – This link locates gene lists saved in caIntegrator.
• Click the gene list:search;searching:gene list;list:searching geneGenes List icon ( ) to open the Gene List Picker dialog box. For more information, see .
• In the drop-down menu that lists previously saved gene lists, select a gene list. In the list that appears, use the check boxes to identify the genes whose symbols you want to use in the gene expression analysis.
• GISTIC Amplified genes is a list of gene symbols in which the corresponding regions of the genome are significantly amplified.
• GISTIC Deleted genes is a list of gene symbols in which the corresponding regions of the genome are significantly deleted.
• Click Use Genes at the bottom of the dialog. This pulls the checked genes into the Search Criteria tab.
• CGAP, genes search;searching:CGAPCGAP – Use this directory to identify genes. Before clicking this link you must enter gene symbols in the text box. This link does not pull anything into caIntegrator but does provide information about the gene(s) whose names you entered.

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Editing a Gene or Subject List

editing:gene list;gene list:editing;gene list:deletinggene list:viewing:list:deleting gene;list:editing geneTo 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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Once a list is created, you cannot edit the list contents. AnchorRTF38303736393a204865616469RTF38303736393a204865616469

Editing a GISTIC Analysis*

To
editing:GISTIC analysis results;GISTIC:editing analysis resultsTo view a GISTIC analysis page in caIntegrator where you can review or edit analysis parameters and results, under Study Data in the left sidebar, click Saved Copy Number Analysis. Select the analysis you want to open. The system displays analysis parameters and gene lists that that were retrieved from the analysis ().

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As long as you leave this analysis in the study, caIntegrator lists the genes retrieved from the analysis in the Gene Picker dialog box when you open it.
See also and .
Expanding

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• View in NBIA – search results:viewing imaging data in NBIA;NBIA:viewing imaging results inThis link corresponds to each Image Series listed in the results table. If you click the link, NBIA opens to the login page. After you log in, NBIA brings up the first image in the corresponding image series (). You must log into NBIA to see the data. On the NBIA page that opens, you can opt to view the entire series containing this image, or you can display the image as a large JPEG-formatted image. You can also add the image to the NBIA basket. For more information, see the NBIA online help or user's guide accessible from NBIA.

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  An example of displaying the first image in image series
• Forward to NBIA – search results:forwarding imaging results to NBIA;NBIA:forwarding imaging results toThis 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.

See also and
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Retrieving DICOM Images

On thesearch results:retrieving DICOM images;DICOM, retrieving images the 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 (). For more information, see the note below.

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Click the Download DICOM link to download and save the file. caIntegrator unzips the file and displays the list of images in the file. To open the DICOM images, you must have a DICOM image viewer application installed on your computer. For more information, see .
In the search results, not all of the patients in the data subset may be mapped to image series IDs. If you select a mixture of patients that have image annotations as indicated by an image series ID and patients that do not have image annotations (no image series ID), when you click the Retrieve DICOM Images button, NBIA retrieves the images for the entire NBIA study instance UID that includes the image seriesIDs you checked.
If on the Search Results tab you select only patients that have image annotations as indicated by an image series ID, when you click the Retrieve DICOM Images button, NBIA retrieves images for the NBIA image series that were matched in the search. If the results are a mixture, but you select one specific row with a valid image annotation, caIntegrator aggregates to the image series. If results are a mixture and you select multiple rows, caIntegrator aggregates to the NBIA study in which multiple image series you have selected in the search results are found.
If your query does not have image annotations and all check boxes are selected, results will go up to image series UID and gives all image series in it. Search results may ultimately depend on how the study was created. For example, if no image series display in query results, it means they were not mapped in the study. In that case, the results "move" up to Study Instance UIDs. See
To best understand this, it is important to review the hierarchy of submissions in NBIA. For more information, see .
See also
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Example of Retrieving Images:*

If you images:example of retrievingare 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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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. AnchorRTF38343139303a204865616469RTF38343139303a204865616469

Relationship of Patient to Study to Series to Images

patient, relationship to study, series, images;study:relationship patient, study, series, imagesThis This flowchart illustrates the relationship of patient to study to series and lastly to images.

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• All image details (name, size, etc.)
• The series that the image belongs to
• Image feature attributes
• The subject ID. Click the subject ID under Annotations on the Results Type tab to display this.

See also .
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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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