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For more information about CGHCalls, see Continue with step in .

Choosing Genes

caIntegrator provides three methods whereby you can obtain gene names for a gene expression search.

• caBIO – This link searches caBIO, then pulls identified genes into caIntegrator for analysis.
  1. Click the caBIO icon ( Image Removed).
  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. Image Removed
  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. Image Removed
• Gene List – This link locates gene lists saved in caIntegrator.
  1. Click the Genes List icon (Image Removed) to open a Gene List Picker dialog. For more information, see on page 69.

If a GISTIC analysis has been run, you may see the following options:

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• • GISTIC Amplified genes is a list of gene symbols in which the corresponding regions of the genome are significantly amplified.
  • GISTIC Deleted genes is a list of gene symbols in which the corresponding regions of the genome are significantly deleted.

1. In the drop-down menu that lists previously saved gene lists, select a gene list. In the list that appears, use the check boxes to identify the genes whose symbols you want to use in the gene expression analysis.
2. Click Use Genes at the bottom of the dialog. This pulls the checked genes into the Search Criteria tab.

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Query Results

You can specify columns for the way you want the search results to display either before or after you run the search. If you run the search directly from the Criteria tab before setting the results type/sorting features, by default only the Subject Identifiers display on the Search Results tab. You can then come back to the and to expand the display options and re-run the search, having set the display parameters.
For more information, see on page 65.

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