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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. 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. !worddavb0c0bc712982eb0268f4f1837af797ae.png|vspace=4, alt="Search page"!

3. On the Criteria tab, in the drop-down list, select the type of data you want to search (), as shown in the following figure.
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.

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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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• caBIO – This link searches caBIO, then pulls identified genes into caIntegrator for analysis.
  1. Click the caBIO icon ( ).
  2. 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'.
  3. 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.
  4. 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.
  5. Choose the Taxon from the drop-down list and click Search. The search results display (), as shown in the following figure.
  6. In the search results, use the check boxes to identify the genes whose symbols you want to use in the gene expression analysis.
  7. Click Use Genes at the bottom of the page. This pulls the checked genes into the Criteria tab (), shown in the following figure.
• Gene List – This link locates gene lists saved in caIntegrator.
  1. Click the Genes List icon () to open a Gene List Picker dialog. For more information, see on page 69.

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The selection you make on the Results Type tab determines whether caIntegrator displays search results for subject annotation or genomic data. It filters the search based on the criteria you set on the Criteria tab, whether it is annotation, gene expression or image series data type(s). In other words, if you select annotation criteria on the Criteria tab, but select Genomic on the Results Type tab, the data subset that displays on the Search Results tab is genomic data that is filtered by the annotation criteria you defined on the Criteria tab.

1. 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.

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

   Results display as tabular data.
   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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1. 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 this table ()the table shown in the following figure.
2. In the Row Order column, indicate how you want columns sorted, Ascending or Descending, or leave the default, No Sort, if you choose.
3. 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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