Support for IPA
Support for this pathway analysis tool is provided as standard.
About this plug-in
IPA (Ingenuity Pathway Analysis) is a commercial web-based software application for the analysis, integration and interpretation of data derived from any experiments that generate gene and chemical lists with expression data, such as metabolomics and proteomics. It leverages the expertly curated Ingenuity Knowledge Base, reviewed for accuracy by PhD scentists.
For licensing terms, please visit the IPA website.
Using the tool
First, make sure that you can launch IPA using the default browser on your system. The plug-in relies on the browser to upload the Progenesis-exported data to IPA.
The export works with protein identifications matching the current protein tag filter.
For over-representation analysis and other types of analyses that do not make use of protein expression data, it's possible to create a list of proteins in IPA. You need to select the type of protein identifiers used in your experiment. If there are proteins with different identifier types, filter the protein list to contain only proteins with single identifier type at a time, then perform the export operation and merge the resulting lists in IPA.
The IPA list creation options.
For enrichment analysis and other types of analyses that require protein expression data, you upload a protein expression dataset to IPA. You need to select the type of protein identifier used by at least one protein whose expression data you want to export. If there are proteins with different identifier types, you will be able to select additional identifier types in IPA after the dataset is uploaded. The operation exports data from a single observation at a time - select the two experimental conditions (taken from the current experiment design) you wish to compare as that observation.
The IPA dataset upload options.
After you select the appropriate options, click the "Export proteins to IPA" button. Your default web browser should open and after it uploads the exported data to IPA, it should download a file with .JNLP extension. If your browser is not set up to launch this kind of file automatically, do so manually and the IPA software should open, showing the uploaded data.
Troubleshooting
When I click the "Export proteins to IPA" button, the browser opens and displays an IPA page saying that "This session has been expired (possibly due to multiple concurrent logins being attempted as the same user)". When I click "Continue", it displays a different IPA page saying "Missing required parameter: geneid". What should I do?
This message is shown if the IPA session in your browser has expired, or, for some browsers (most notably Internet Explorer), cannot be reused for data upload. Close your running IPA instances, if any, click "Continue" and, after logging in, retry the export operation from Progenesis.
When I click the "Export proteins to IPA" button, the browser opens and displays an IPA page saying "Unable to map to <id> for any requested gene identifiers". What should I do?
You need to select the identifier type used by at least one of the exported identifications and the identified protein must exist in the IPA database (which you can confirm in the IPA software itself).