Bioinformatics Software: Ingenuity Pathway Analysis (IPA)

Ingenuity Pathway Analysis (IPA) is a web-based functional analysis tool for omics data.

Making Sense of Your Omics Data

• Identify the most relevant signaling and metabolic pathways, molecular networks, and biological functions for list of genes
• Predict the direction of downstream effects on biological and disease processes
• Predict the activation and inhibition of upstream transcription factors
• Compare affected pathways and phenotypes across multiple testing conditions

Search and Explore Biological and Chemical Knowledge

• Quickly gain knowledge on genes and chemicals by browsing categorized and curated publications
• Dynamically build and explore bio-molecule interaction networks supported by literature findings
• Identify potential biological impacts of custom networks
• Generate testable hypothesis for your genes of interest

IPA is one of the best functional analysis and knowledge discovery tool.  It is widely used by the life science community. 

• Up-to-date high quality knowledgebase manually curated by PhD scientists
• Search for targeted information on genes, proteins, chemicals, and drugs
• Extensive library of well-characterized signaling and metabolic pathways offer a starting point for exploration and a bridge between novel discovery and known biology. Layer in novel insights, drugs, and 'omics data.
• Extensive knowledge database on model organisms human, mouse, rat. Additional species supported via ortholog mapping.
• Easy and flexible collaboration and results sharing.

USC has licensed IPA for the free use of USC faculty, students and staff. The license consists of THREE concurrent user seats.  To get an account and access IPA account:

1. Carefully read the IPA user policy
2. Fill out and submit the IPA registration form
3. Activate your account following the link in the confirmation email from the Ingenuity Systems (may take 1-2 business days)
4. Download IPA client launcher.
5. Log in with the IPA client. 

Get started with video tutorials

• Introduction to IPA (34min)
• Formatting and Uploading Data into IPA (38min)
• Search and Explore in IPA (38min)
• Understand biological mechanisms with IPA Core Analysis and Analysis Match (40min)
• Tips and Tricks for performing RNA-Seq Analysis in IPA (37min)
• Tips and Tricks for performing miRNA Analysis in IPA (35min)
• Exploring the Upstream Analysis results in IPA (40min)
• Identify Key Isoforms in your RNA-seq datasets with IsoProfiler (36min)

Help @ Ingenuity Systems

• Check out the online help page for a wealth of useful information, including case studies, white papers and FAQs
• Contact Ingenuity support
  • by phone: 866.464.3684 (6am - 5pm PST)
  • by email: ts-bioinformatics@qiagen.com
• Additional resources including webinar archives

Help @ USC Libraries Bioinformatics Service

• Email us: nmlbio@usc.edu​