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This chapter describes the processes for searching studies within caIntegrator.

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1. In caIntegrator, in the upper right hand corner, select the study you want to browse or perform a simple search.
2. On the left sidebar, under the first section that displays the study name, click Search [Study Name]. This opens a simple search query page with five tabs.
3. On the Criteria tab, shown in the following figure, in the drop-down list, select the type of data you want to search.
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4. You can perform a search using one or more criteria you set in one of the data types, or you can define criteria in more than one data type per query, creating a more complex search.
   • Annotations (listed as 'default' or by annotation group name when specified when the study was created)
   • Gene Expression or Copy Number
   • Image Series
5. Click Add to further define criteria for the search.
   Continue with:
   Annotation and Image Data Searches
   Gene Expression Searches
   Copy Number Searches
   CGHCalls Searches
6. To add additional criteria for the search, repeat steps 4 and 5, as appropriate. You can set more than one data type or more than one criterion for a data type. The criteria become cumulative, thus refining the search.
7. Once you have configured the query criteria, select the Boolean Or or Andsearch operator at the bottom of the page.
   • Or finds a data subset with at least one of the search criteria
   • And finds a data subset with both/or all search criteria.
8. Click the Remove button to clear any data elements you have defined.
9. You can launch the search from this Criteria tab. Click the Run Search button. For information about the search results, see 5 - Viewing Query Results. You may want to run the search first to see what kind of results you get before you configure the data display, described in step 10.
   – or –

10. On the Results Type tab, you can specify the columns you want to display in the search results data. On the Sorting tab, you can specify how the data is to be sorted. For more information, see Results Type Tab and Sorting Tab.

    Note
    title Be Careful
    As long as you are still in the current query session, you can return to the Criteria, Columns and Sorting tabs to add, modify or remove data and display criteria and re-run the search. If you configure another query without saving the first, the first query will be lost. If you save the query, your current search criteria are saved.

Annotation and Image Data Searches

Once you select an annotation group data type, an additional drop-down list displays data elements that are annotation definitions specified for that data type when the data was uploaded into the study. An example is shown in the following figure.
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1. Select a search criterion from among the options. You can make only one selection at a time.

   Info
   title For imaging searches
   If the study includes imaging data, imaging annotations should be available in the Annotations list, as shown in the following figure.

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2. Each choice opens other fields relevant to the selection where you can further define your search query.
   • If permissible values were added when the annotation was defined, you must select among the values in a drop-list that displays on the right side of the page. An example is shown in the following figure.

   • If no permissible values were defined as part of the annotation, you have the option to enter descriptive text in a text box on the right side of the page.
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     Note
     title Caution
     When working with image data, if only an imaging mapping file was uploaded when the study was created and not an image series annotation file, you cannot enter image search criteria. The search results will, however, display a link that allows you to view the associated images in NBIA.

3. Continue with step 6 in Searching a caIntegrator Study.

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Expression Level Selection

Additional fields display for the Expression Level selection.

1. Select the range type from the following options:
   
   • >=: Greater than the entered value
   • <=: Less than the entered value
   • Inside Range: Looks for all matching values that occur between the two levels you enter
   • Outside Range: Looks for all matching values that are not in between the two levels that you enter.
     The range of possible values is determined on the array side; the value is affected by the array type and the sample's behavior.
2. Enter the Expression Level appropriate for your query. The value that you enter is compared to the expression levels that are reported by the probes on the array platform. The probe value is typically a normalized value.This criteria changes slightly based the range type you select.
   The default value of 100 is a fixed default and does not reflect any values on the array. It simply represents a starting point for the query.
3. Continue with step 6 in Searching a caIntegrator Study.

Fold Change Selection

Additional fields display for the Fold Change selection. The fold change option appears only if genomic control samples have been uploaded to the study. Fold change identifies genes with expression differences compared to control samples, as defined when the study was deployed in caIntegrator. You can enter query values in greater/lesser-than-or-equal-to arguments.

1. Select or enter data for the Fold change fields shown in the following figure and described below.
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   • Gene Symbol - See Gene Names Search.
   • Control Sample Set – If multiple platforms are part of the study, your platform selection in the Fold Change query criteria determines the control samples that are available.
     Select from the drop down list the name of the uploaded control sample set to serve as the fold change reference.
   • Regulation Type – Select the term that describes the gene expression in comparison with the control samples: Up is increased expression; Down is decreased expression; Up or Down is increased or decreased; Unchanged means no change in expression.
   • Up-regulation Folds – Enter a numerical value representing fold change. The number you enter here is dependent upon the Regulation Type you selected.
     
     • Up = Up Regulation Folds – Samples with a fold change greater than this value, when compared to the control samples, will be returned.
     • Down = Down Regulation Folds – Samples with a fold change less than this value, when compared to the control samples, will be returned.
     • Up or Down = Down Regulations Folds, Up Regulation Folds – Samples with a fold change either up or down, when compared to the control samples, will be returned.
     • Unchanged = Samples with a fold change between the two specified values will be returned.
       For example, if you enter 2.0 in this field, after selecting Up in the previous field, the search will locate genes whose expression is 2 times (2-fold up regulation) the base value.
2. Continue with step 6 in Searching a caIntegrator Study.

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1. Select or enter data for the copy number query fields shown in the following figure and described below.
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   • Segment Mean <= – Enter the value equal to or less than the higher limit of change.
   • Segment Mean >= – Enter the value equal to or greater than the lower limit of change.
   • Genome Interval > Gene Name – See Choosing Genes.
   • Genome Interval > Chromosome Number – In the text box that opens, enter the chromosome number you want the query to search against.
   • Genome Interval > Chromosome Coordinates – In the From and To text boxes that open, enter the range on the chromosome you want to search. This defines the chromosomal boundaries of the region with the suspected copy number variations.
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     The Bioconductor DNAcopy algorithm (see Copy Number Data) identifies the location of the amplification or deletion and then reports it as the base pair at the start and stop of the segment. Each segment is then catalogued with chromosome number, start coordinate, stop coordinate, genes in the segment, and the segment mean value.
   • To search for Gene Symbols, see Choosing Genes.
2. Continue with step 6 in Searching a caIntegrator Study.

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1. Select or enter data for the copy number query fields shown in the following figure and described below.
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   • Copy Number values: Select one or more of the Calls values. Values are -1 (loss), 0 (normal) or 1, (gain). If four levels were used for calling, a value of 2 represents an amplification.
   • Genome Interval > Gene Name – See Gene Names Search.
   • Genome Interval > Chromosome Number – In the text box that opens, enter the chromosome number you want the query to search against.

   • Genome Interval > Chromosome Coordinates – In the From and To text boxes that open, enter the range on the chromosome you want to search. This defines the chromosomal boundaries of the region with the suspected copy number variations.
     For more information about CGHCalls, see CGHcalls

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   • To search for Gene Symbols, see Choosing Genes.
2. Continue with step 6 in Searching a caIntegrator Study.

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1. On the Results Type tab, shown in the following figure, select the Annotation, Copy Number or Genomic radio button to search annotation data. Search criteria are described below.
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2. Annotation- Select the annotation elements that you want to display in the search results. All elements listed are column headers in the data uploaded to the study. You can make multiple selections on this list.

   Info
   title Default display
   For subject annotations, the Patient or Subject Identifier displays by default in the search results.

   
   Results display as tabular data.

3. Copy Number - This option appears only if the open study includes copy number data. If you select this option, the annotation elements initially displayed on this tab disappear, and you are asked to run the query again. Based on the criteria you defined, the Query Results tab shows a data matrix containing samples against the genomic region you specified. For more information, see Copy Number Searches and Copy Number Data.
4. Gene Expression - Select the Reporter Type and Results Orientation.
   
   • Gene Name – Finds and summarizes at the gene level all reporters that match criteria for the gene you defined on the Criteria tab
   • Reporter ID – Finds all reporters that map to the gene(s) you identified on the Criteria tab
   • Genes in rows/Subjects in columns or Genes in columns/Subjects in rows – Determines query results matrix format
     Results display in a gene expression data matrix. For more information, see Gene Expression Data.

5. Imaging - If imaging annotations have been added to the study, annotation elements also display on the lower right section of this page when you select Annotation. All elements listed are column headers in the image annotation data uploaded to the study. You can make multiple selections on this list.

   Info
   title Image series IDs display
   If you select even one Image Annotation on the Results Type tab, the Image Series IDs display by default in the search results. If you select no Image Annotations on the Results Type tab, however, even if you have selected image series criteria on the Criteria tab, no image series IDs display in the search results. The fact that images can be located, however, in NBIA is indicated by two image-related buttons at the bottom of the Query Results page. You can open the images in NBIA, but they will be at StudyInstance UID level. See Relationship of Subject to Study to Series to Images.

6. Use the Select All or Unselect All buttons to aid you in making your selections.
   Results display as tabular data. For more information, see Subject Annotation and Imaging Data.

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After running a search, you can export the result set or a subset as a tab-delimited text file. For more information, see Exporting Data.

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