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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.- On the Criteria tab, shown in the following figure.
!criteria tab80.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.
Continue with:
#Annotation and Image Data Searches
#Gene Expression Data Searches
#Copy Number Searches - To add additional criteria for the search, repeat steps and , 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.
- Once you have configured the query criteria, select the Boolean Or or And search 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.
- Click the Remove button to clear any data elements you have defined.
- You can launch the search from this tab. Click the Run Search button. For information about the search results, see . 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 .
– or – - 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 and .
Info title Note 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.
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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. 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, 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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caIntegrator provides three methods whereby you can obtain gene names for a gene expression search. See #Choosing Genes.
Expression Level Searches
Additional fields display for the Expression Level selection.
Range Type –
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Additional fields display for the Fold Change selection.
Fold Change Searches
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.
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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.
Continue with step in .
Copy Number Searches
In some diseases, like cancer, cells that are abnormal can exhibit a change in the chromosomal structure in that parts of a chromosome can be amplified or deleted. 'Copy number' experiments that measure variation in genomic structure use molecular markers to detect amplification or deletion of chromosomal segments. Typically, copy number alteration experiments compare a genomic sample from a diseased tissue (for example, a tumor) to a control sample (for example, blood).
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caIntegrator provides three methods whereby you can obtain gene names for a copy number search. For information about selecting genes, see #Choosing Genes.
Segmentation Searches
Additional fields display for the Segmentation selection.
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caIntegrator provides three methods whereby you can obtain gene names for a copy number search. For information about selecting genes, 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.
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.
CGH Calls Searches
Additional fields display for the Calls selection.
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caIntegrator provides three methods whereby you can obtain gene names for a copy number search. For information about selecting genes, 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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- 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.
- 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.
- 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
Results display in a gene expression data matrix. For more information, see on page 66.
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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.
Sorting parameters are saved as part of the query if you choose to save it using the Save Query feature. See . - If you click the Reset button before running the query from the Sorting tab, the original column settings are restored.
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