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Qiagen Ingenuity Pathway Analysis (IPA)

Description

Ingenuity Pathway Analysis (IPA) (Qiagen) IPA works with differential expression data (derived from RNA sequencing, miRNA sequencing, microarray, proteomics, phosphoproteomics, or metabolomics) or genetic variant data to extract various biological insights.

Listing of Analysis Functions

  • Discern affected molecular biology pathways and networks
  • Provide insight on regulatory mechanisms including upstream regulators driving gene expression
  • Predict effect on disease and function
  • Reveal biomarkers and drug targets
  • Identify miRNA targets
  • Compare results against similar studies

Recommendations

IPA and CLC Genomics Workbench are both Qiagen products, which allows us to more easily extract biological insight from analysis. For this reason, it is beneficial to use these two packages together.

Things to Know

IPA provides an abundance of curated molecular bioscience information obtained from literature and databases. The curated content can be mined to gain insight and facilitate hypothesis generation.

Input Data Types

IPA takes tabular data as input. Differential gene expression data should contain columns with gene names, log fold change, and p value. We can also provide a table with genetic gain/loss of function information if this is the topic of our study. Thus, IPA is able to import files with the following extensions:

  • XLSX
  • XLS
  • CSV
  • Tab delimited TXT

Output Data Types

  • Visualizations can be exported as the following under various resolutions
  • PNG
  • PDF
  • Tabular data can be exported as
  • Tab delimited TXT
  • XLS

Access Information

You must submit a request through service.cancer.gov to obtain access to Qiagen IPA. This software requires access to a floating license server, and so care should be taken to return licenses when the software is not actively being used (i.e., close the application). OSTR holds 6 concurrent licenses to IPA. Users must be either on the NIH network or connected via VPN if remote.

Getting Help

Qiagen IPA comes with extensive help documentations, tutorials, and video tutorials.