Process Description

Ingenuity Get Gene Pathways

The Ingenuity Get Gene Pathways process retrieves all of the pathway identifiers for all of the genes in the input data set and creates a new column containing them. The new column includes the delimiter " / " to separate the pathway identifiers, and is suitable for use with the Gene Set Enrichment and Gene Set Scoring processes, or for general searching.

Note: This process is considered experimental.

What do I need?

Two files are required to run the Ingenuity Get Gene Pathways process:

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A SAS Input Data Set that must contain a variable with valid Entrez gene identifiers. The u95a_significant_differences.sas7bdat data set serves as an example, and is shown below. This data set contains numerous variables listing various gene identifiers.

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The Ingenuity Canonical Pathway Membership Data file. This CSV file, which can be downloaded from Ingenuity, lists the identifiers, nodes, and associated genes for each pathway in the Ingenuity database.

Note: If you are an IPA user who needs help with downloading the Ingenuity pathway list, contact Ingenuity customer support by e-mail at support@ingenuity.com.

The u95a_significant_differences.sas7bdat data set is located in the Sample Data\Microarray\Affymetrix Latin Square directory included with JMP Genomics. The IngenuityIdList.xls Ingenuity pathways file was downloaded from Ingenuity and placed in the C:\Program Files\SASHome\JMPGenomics\13\Genomics\Testing\ThirdPartyAnnotation folder created for this example.

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

Output/Results

Refer to the Ingenuity Get Gene Pathways output documentation for detailed descriptions of the output of this process.