IpaNewPathway.pdf

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Create New Pathway (Ingenuity)

Note: The Create New 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 "Create New Pathway" command allows the user to upload a list of identifiers to Ingenuity Pathway Analysis (IPA), and create a new pathway within Ingenuity for further analysis. The Ingenuity Create New Pathway command will open the Create New Ingenuity Pathway window:

IPANewPath0.png

For this module, 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).

General

Input/Output

  • The window includes a dropdown box to select the Project and Data object on which the command will be run.
  • The Rows option allows the user to select the rows to be used in building the Ingenuity pathway.

Options

The following options are available to describe the data set:

  • ID column - Allows the user to select the appropriate column that will be used as the identifier (the default is Probe Set ID). The user to choose any column in a 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 (the default is affymetrix). Available ID types include abi, affymetrix, affymetrixsnp, agilent, codelink, entrezgene, genbank, genpept, ginumber, hugo, illumina, ipi, locuslink, refseq, swissprot, and unigene.
  • The user can specify the Project name under which the pathway should be created.
  • Optionally, the user can specify the name of the new pathway, using the Pathway name

Clicking Submit will submit the data for creation of a new Ingenuity pathway. Note: There is a limit of 250 genes that can be uploaded at one time to IPA using this tool.


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