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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, in the drop-down list, select the type of data you want to search.
- 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
#CGH Call Searches - 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.
- 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 Criteria tab. Click the Run Search button. For information about the search results, see #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 – - 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.
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 for that data type when the data was uploaded into the study. An example is shown in the following figure.
- 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.
- 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.
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.
- Continue with step 6 in Searching a caIntegrator Study.
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- Select or enter data for the Fold change fields shown in the following figure and described below.
- 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.
- Up = Up Regulation Folds – Samples with a fold change greater than this value, when compared to the control samples, will be returned.
- Continue with step 6 in Searching a caIntegrator Study.
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- Select or enter data for the copy number query fields shown in the following figure and described below.
.- 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 #Gene Name 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.
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.
- Segment Mean <= – Enter the value equal to or less than the higher limit of change.
- Continue with step 6 in Searching a caIntegrator Study.
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- Select or enter data for the copy number query fields shown in the following figure and described below.
- 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. - To search for Gene Symbols, see Choosing Genes.
- Continue with step 6 in Searching a caIntegrator Study.
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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 #Saving a Query. - If you click the Reset button before running the query from the Sorting tab, the original column settings are restored.
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