IpaGcpView.pdf

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View Canonical Pathway (Ingenuity)

Note: The View Canonical Pathway menu item and all menu items found within the Expression Menu can only be performed on Data objects. It is assumed that the user has a fully functional Ingenuity account, that can be launched using Web Start mode.

The "View Canonical Pathway" command will take a list of identifiers in Array Studio and search against the Ingenuity Canonical pathways. Selecting this option will present the following window:

IPAGcpView0.png

General

Input/Output

  • The window includes a dropdown box to select the Project and Data object on which the command will be run. Any type of Table or Data can be used (the Data selected in the dropdown box will allow the user to specify in the Options section the ID column to be used for uploading to IPA--for instance, from an Inference Report, Table, or Data object).
  • The Rows option allows the user to select which rows should be included in the upload (options include all, selected, visible, and any pre-generated Lists). The user should select the List of variables/genes/etc.. to upload here.

The following options are available to describe the data set:

Options

  • ID column - Allows the user to select the appropriate variable column that will be used as the identifier (the default is Probe Set ID) from any Table or Inference object, as well as any column from the Annotation Table of a Data object.
  • ID type - This value describes the type of identifier that has been selected in the previous step . Available ID types include: abi, affymetrix, affymetrixsnp, agilent, codelink, entrezgene, genbank, genpept, ginumber, hugo, illumina, ipi, locuslink, refseq, swissprot, and unigene.

Selecting the "Submit" button will launch Ingenuity and perform the search.

Note: The View Canonical Pathway command can take no more than 250 genes. The user may be asked to sign in to Ingenuity before proceeding.

OmicScript

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