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- In caIntegrator, in the upper right hand corner, select the study you want to browse or perform a simple search.
Wiki Markup 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, shown in the following figure. !criteria !worddavb0c0bc712982eb0268f4f1837af797aetab80.png|vspace=4, alt="Search page"!- On the Criteria tab, in the drop-down list, select the type of data you want to search, as shown in the following figure.
- 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
- Click Add to further define criteria for the search.
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- Once you select an annotation group data type, an additional drop-down list displays data elements that are annotation definitions specified when the data was uploaded into the study, as shown in the following figure.
- Select a search criterion from among the options. You can make only one selection at a time.
Info title Note If the study includes imaging data, imaging annotations should be available in the Annotations list.
- 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.
- 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, shown in the following figure.
Info title Note 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.
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- Select or enter data for the Fold change fields shown in
: the following figure and described below.
- Control Sample Set – 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.
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- Select or enter data for the copy number query fields shown in the following figure.
Segmentation is the process of defining the chromosomal boundaries (coordinates) of the region deleted or amplified in the sample.
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- 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.
The Bioconductor DNAcopy algorithm (see on page 68) 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.
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- Select or enter data for the copy number query fields shown in the following figure and described below.
CGHCalls calls aberrations for array CGH data using a six state mixture model.
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- On the Results Type tab, shown in the following figure, select the Annotation, Copy Number or Genomic radio button to search annotation data.
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.
Results display as tabular data.Info title Note For subject annotations, the Patient or Subject Identifier displays by default in the search results.
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 and on page 68.
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
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- Select the Sorting tab and indicate the left to right column order of the Search Results by changing one or more numbers in the Column Order column in the table shown in the following figure.
- In the Row Order column, indicate how you want columns sorted, Ascending or Descending, or leave the default, No Sort, if you choose.
- Click Run Query at the bottom of the page to execute your sorting changes in the search results. When you do so, the change in column order is visible on the Query Results tab, as well as on the Sorting tab. For example, any column that you have indicated to be number "1" now appears in Query Results immediately after the Subject Identifier column and at the top of the Set Sort Order table on the Sorting tab.
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- Select it in the left sidebar under the Study Data > Queries > My Queries.
- Click the Edit icon (
) corresponding to the study. - Change the query and display criteria on the Criteria, Columns and Sorting tabs.
- On the Save As tab, check the appropriate options and click Save As. You can use the same name as the original query or modify the name as needed.
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