Model, analyze, and understand the complex biological and chemical systems at the core of life science research with IPA

Causal Network
Market Leading Pathway Analysis
Unlock the insights buried in experimental data by quickly identifying relationships, mechanisms, functions, and pathways of relevance.
Causal Network
Predictive Causal Analytics
Powerful causal analytics at your fingertips help you to build a more complete regulatory picture and a better understanding of the biology underlying a given gene expression study.
RNA Seq Data Analysis
NGS/RNA-Seq Data Analysis
Get a better understanding of the isoform-specific biology resulting from RNA-Seq experiments.

Peer Reviewed and Widely Adopted

QIAGEN’S Ingenuity Pathway Analysis (IPA) has been broadly adopted by the life science research community and is cited in thousands of peer-reviewed journal articles.


Comparison Analysis.

Quickly visualize trends and similarities across analyses using heat maps for Canonical Pathway, Downstream Effects, Upstream regulators and Causal Network Analyses. Prioritize by score, hierarchical cluster or trend.

Comparison Analysis

More content to better interpret RNA-Seq datasets.

Insights gleaned from IPA analysis of RNA-Seq data demonstrate a greatly improved workflow for reseachers to proficiently handle RNA-Seq data and generate testable hypotheses. The latest release contains Mouse isoform information from either Ensembl or RefSeq (in addition to human).

Mouse isoform - Ingenuity IPA

Understand Complex ‘Omics Data

IPA helps you understand complex ‘omics data at multiple levels by integrating data from a variety of experimental platforms and providing insight into the molecular and chemical interactions, cellular phenotypes, and disease processes of your system.

Understand Complex 'Omics Data Graphic - Ingenuity IPA

Advanced Features

Powerful features in IPA, Causal Network Analysis, BioProfiler and My Findings will help you understand causal connections between diseases, genes networks of upstream regulators and leverage your own domain expertise and proprietary curation efforts.

Advanced Features- Ingenuity IPA

Unlock the Value of your Experiments

Analyze, integrate, and understand data derived from gene expression, microRNA, and SNP microarrays; metabolomics, proteomics, and RNA-Seq experiments; and small-scale experiments that generate gene and chemical lists with IPA.

Casual Connettion Graphic - Ingenuity IPA

See What Customers Are Saying About IPA

"We've recently seen that genes associated with critical cellular functions are often regulated post-transcriptionally. Ingenuity's Upstream Regulator in IPA allows for the identification of these important regulators from expression data sets and is going to completely change the field of bioinformatics by identifying these potential regulators and not limiting the analysis to just the transcriptome."

Michael Edwards, Ph.D., Assistant Professor, UC Denver

Picture of Michael Edwards, Ph.D., Assistant Professor, UC Denver
Ingenuity IPA Interpret Biological Meaning Graphic

Quickly analyze your data to identify key insights with IPA

IPA can help with almost any transcriptomics-related question or application
Biomarker Discovery
Identifies the most promising and relevant biomarker candidates within experimental datasets
microrna research
microRNA Research
Combines filtering tools and microRNA-mRNA content to provide insight into the biological effects of microRNAs
Delivers a focused toxicity and safety assessment of candidate compounds, and provides a more complete understanding of pharmacological response, drug mechanism of action, and mechanism of toxicity
Overcomes the metabolomics data analysis challenge by providing the critical context necessary to gain biological insight into cell physiology and metabolism from metabolite data
drug repositioning
Drug Repositioning
Expression profiling of approved drugs and comparison to profiles of diseased tissue can lead to discovery of new uses for these already approved entities
Perform a comprehensive analysis of your proteomics for a deep understanding of proteins and related biological processes
target discovery
Target Discovery
Genes that are shown to be activated in a pathological condition may serve as promising targets for therapeutic development efforts

The Ingenuity Knowledge Base

knowledge base graphic

All of Ingenuity’s solutions leverage the Ingenuity Knowledge Base, a repository of expertly curated biological interactions and functional annotations created from millions of individually modeled relationships between proteins, genes, complexes, cells, tissues, drugs, and diseases. These modeled relationships, or Findings, include rich details, links to the original article, and are reviewed for accuracy by PhD scientists. The curated content in the Knowledge Base is structured into an Ontology that allows for contextual information, computation by the applications, and synonym resolution to ensure consistency across concepts. These features make the Ingenuity Knowledge Base distinctive and unparalleled to any other database.

IPA has a broad set of features that allow you to quickly understand and visualize your data

Comparison Analysis

Quickly visualize trends and similarities across analyses using heat maps for Canonical Pathway, Downstream Effects, Upstream regulators and Causal Network Analyses. Prioritize by score, hierarchical cluster or trend.

Human and Mouse Isoform View

Understand the structure and function of both human and mouse isoforms (splice variants). For each gene, toggle between human or mouse RefSeq and Ensembl to visualize associated isoforms on the Isoform View.

Regulator Effects

Provides insights into your data by integrating Upstream Regulator results with Downstream Effects results to create causal hypotheses that explain what may be occurring upstream to cause particular phenotypic or functional outcomes downstream.

Causal Network Analysis

The new Causal Network Analysis provides a comprehensive approach to identifying upstream molecules that control the expression of the genes in your datasets. Expanding beyond "direct" or "single hop" relationships between the upstream regulator and the target molecules in the dataset, Causal Networks uncovers networks of regulators that connect to the dataset targets. Focus on the networks that are of highest relevance by scoring the resulting causal networks against molecules or diseases/functions of interest.

Disease View

Provides details associated with the disease or biological function such as molecules associated with that disease or function, known drug targets, drugs known to target those molecules, and more.

Interactive Disease and Functions Nodes

Interactive visual exploration of causality between molecules and disease, function, or phenotypes from a network or My Pathway.


Quickly profile a disease or phenotype by understanding its associated genes and compounds. Identify genes known to be causally relevant as potential targets or identify targets of toxicity, associated known drugs, biomarkers and pathways.

Upstream Regulator Analysis

Predict upstream molecules, including microRNA and transcription factors, which may be causing the observed gene expression changes.

Mechanistic Networks

Automatically generate plausible signaling cascades describing potential mechanism of action leading to observed gene expression changes.

Downstream Effects Analysis

Identify whether significant downstream biological processes are increased or decreased based on gene expression results.

Pathway Analysis, Canonical Pathways, Overlapping Pathways, Pathway Import and scoring

Pathway Analysis, Canonical Pathways, Overlapping Pathways, Pathway Import and scoring. Determine most significantly affected pathways.

Network Analysis

Build and explore transcriptional networks, microRNA-mRNA target networks, phosphorylation cascades and Protein-Protein or Protein-DNA interaction networks. Identify regulatory events that lead from signaling events to transcriptional effects.  Understand toxicity responses by exploring connections between drugs or targets and related genes or chemicals.  edit and expand networks based on the molecular relationships most relevant to the project.

MicroRNA Target Filter

Reduce the number of steps it takes to confidently, quickly, and easily identify mRNA targets by letting you examine microRNA-mRNA pairings, explore the related biological context, and filter based on relevant biological information as well as the expression information.  The microRNA Target Filter in IPA provides insights into the biological effects of microRNAs, using experimentally validated interactions from TarBase and miRecords, as well as predicted microRNA-mRNA interactions from TargetScan. Additionally, IPA includes a large number of microRNA-related findings from the peer-reviewed literature.

Tox Lists and Tox Functions

IPA-Tox uses Toxicity Functions in combination with Toxicity Lists to link experimental data to clinical pathology endpoints, understand pharmacological response, and support mechanism of action and mechanism of toxicity hypothesis generation.

Molecule Activity Predictor (MAP)

Interrogate sub-networks and Canonical Pathways and generate hypotheses by selecting a molecule of interest, indicating up or down regulation, and simulating directional consequences of downstream molecules and the inferred activity upstream in the network or pathway

Isoform View

Quickly move beyond statistical analysis of high-throughput RNA-Seq data to understand the biological implications of your data.  Identify significantly regulated isoforms in your experiment and determine their potential impact using information about functional protein domains and isoform-specific literature

Gene and ChemView

IPA's Search & Explore capabilities offer researchers access to the most current Findings available on genes, drugs, chemicals, protein families, normal cellular and disease processes, and signaling and metabolic pathways.

Biomarker Filter

Rapidly identify the best biomarker candidates based on biological characteristics most relevant to the discovery study.

Path Designer

Transform your networks and pathways in IPA into publication-quality pathway graphics rich with color, customized text and fonts, biological icons, organelles, and custom backgrounds.  Expand and explore pathways using the high quality content stored in IPA.

Advanced Analytics for Scientists

Powerful features in recent releases of QIAGEN's Ingenuity Pathway Analysis (IPA), Causal Network Analysis and BioProfiler, will help you understand causal connections between diseases, genes networks of upstream regulators and leverage your own domain expertise and proprietary curation efforts.


  • Quickly identify genes known to be causally relevant to a diseases or phenotype as potential drug targets or as targets of toxicity.
  • Find, filter and prioritize genes and compounds by their specific relationships with diseases, phenotypes, and biological functions (e.g. ‘apoptosis’).
  • Gain unprecedented access to the underlying Ingenuity disease and process ontology enabling precise search and filtering of the diseases and phenotypes of interest to you.


Causal Network Analysis:

  • Generates plausible regulatory networks that may explain the gene expression changes in your dataset. These novel upstream regulators control small hierarchical networks that do not require all the molecules to have direct connection to the dataset.
  • Scoring criteria enable you to prioritize the most interesting and relevant hypothesis and quickly visualize the regulatory networks most closely associated with your disease or phenotype of interest.
  • Prioritize resulting hypothesis by molecule, disease, function and/or phenotype of interest. And now discover more distant connections between the causal network and the scoring criteria of interest.
  • Visualize network hypothesis predicted to be responsible for observed expression changes and how it connects to the scoring criteria.
  • See which other master regulators are upstream or downstream of the hypothesis of interest. In addition, export a data matrix of master regulators vs. their targets or master regulators vs. up to 20 analyses.


Relationship Export:

Export relationships from networks and pathways for further visualization

The new Relationship Export capability in IPA enables you to export the structural information contained within IPA networks or pathways for visualization in other tools such as Cytoscape. The export format contains relationships modeled as triples: Node A -> Relationship -> Node B.

In IPA and in Cytoscape

IPA is useful in a wide range of applications at gaining valuable insight into your genomics data

Biomarker Discovery
Identify the most promising and relevant biomarker candidates most relevant to the study within the experimental data.
Contextualize your metabolomics data with rich pathway and process information from the Ingenuity Knowledge Base.
microrna research
MicroRNA Research
Identify the most biologically relevant targets in your microRNA research.
microrna research
NGS/RNA-Seq Data Analysis
Get a better understanding of the isoform-specific biology resulting from RNA-Seq experiments.
Answer the biological questions the researchers you had in mind when you designed your proteomic experiment.
Generate a focused toxicity and safety assessment of candidate compounds that are being examined using toxicogenomics approaches.
Get help with almost any transcriptomics-related question or application.
Causal Network
Causal Network Analysis
Build a more complete regulatory picture and a better understanding of the biology underlying a given gene expression study.

Explore Our Webinars and see how the scientific community has used IPA to create novel discoveries

Presented by: Jean-Noel Billaud, PhD | Duration: 57:58 minutes

Jean-Noel Billaud, PhD, Principal Scientist, QIAGEN Bioinformatics, presents how our in silico solutions enabled us to analyze and identify the biological parameters involved in EEC tumor progression including signaling pathways, biological processes, and potential transcriptional drivers. Read More

Presented by: John A. Martignetti, M.D., Ph.D. and Garry Nolan Ph.D. | Duration: 1:03:20 minutes

Discover how intuitive web-based applications can help scientists quickly analyze and accurately interpret the biological meaning in their genomic data. In the last few years, researchers and clinicians have been faced with the challenge of how to effectively sort through … Read More

Presented by: Dr. Stuart Tugendreich, Scientific Director, IPA | Duration: 34:11 minutes

See the whole picture! Powerful functionality enables you to understand causal connections between molecules and diseases. This Fall 2103 release of QIAGEN’s Ingenuity Pathway Analysis (IPA) has exciting new capabilities which enable interactive visual exploration of causality between molecules and … Read More

Presented by: Dr. Ramon Felciano, Co-founder and Senior Vice President, Applied Research and Partnering, QIAGEN Silicon Valley | Duration: 50:33 minutes

Knowledge of immune system and host-pathogen pathways can inform development of targeted therapies and molecular diagnostics based on a mechanistic understanding of disease pathogenesis and the host response. We used QIAGEN’s Ingenuity platform to investigate the feasibility of rapid target … Read More

Presented by: Dr. Aaron Erdely, Health Effects Laboratory Division, NIOSH and Kaushal Parekh, Associate Staff Ontology Engineer, QIAGEN Silicon Valley | Duration: 36:55 minutes

Metal-rich particulate matter inhalation exposure results in target organ toxicity but also adverse systemic effects including cardiovascular dysfunction and immunosuppression. As a preliminary search for induction of systemic mechanisms, generation of comprehensive transcriptome datasets by DNA microarray, along with gene … Read More

Presented by: Dr. Stuart Tugendreich, Scientific Director, IPA | Duration: 48:24 minutes

The 2013 IPA Spring Release is here! Powerful new functionality enables you to upload, find, and compare datasets, and understand causal connections between diseases, genes, and networks of upstream regulators. Stuart Tugendriech, PhD, Scientific Director, IPA from QIAGEN Silicon Valley … Read More

Presented by: Michael Edwards, Ph.D. Assistant Professor Division of Pulmonary Science and Critical Care Medicine. University of Colorado, Denver | Duration: 40:13 minutes

This webinar discusses an important antitumor pathway in lung cancer (Wnt7a signaling) as a framework to explain the bioinformatic analysis process using IPA. Topics covered include biological function and pathway analysis, network construction, and identifying and interpreting upstream regulators.

Presented by: Dr. Walter Bottje, Professor, Dept. of Poultry Science, University of Arkansas | Duration: 41:26 minutes

Global RNA expression in breast muscle obtained from a male broiler line phenotyped for high or low feed efficiency (FE) was investigated using microarray analysis. By using an overlay function of IPA in which canonical pathways can be projected onto … Read More

Presented by: Aimee Jackson, Ph.D. | Duration: 23:09 minutes

microRNAs are small, non-coding RNAs that function as central regulators of gene expression and development. These regulatory molecules have been implicated in a wide range of normal and pathological activities, including embryonic development, cancer, inflammation, cardiovascular disease and viral infections. … Read More

Ingenuity offers online training with our product technicians and web semimars presented by notable third parties, sign up below!

Ingenuity offers online training with our product specialists and web seminars presented by notable third parties.

During the coming months we’ll be hosting a series of webinars introducing Ingenuity Pathway Analysis.

There is a webinar giving an introduction to IPA. Other sessions will focus on uploading your data, interpreting your results, and there’s an introduction to newly added features. There’s also a webinar on tips and tricks for doing RNA-Seq analysis in IPA.

Our experts Dr. Lynne Mullen and Dr. Jasmin Droege will be hosting the webinars in U.S. and EU time zones, respectively.

documents icon QIAGEN's Ingenuity Pathway Analysis (IPA) Support Documents

The Basics

IPA White Papers – Explore IPA's capabilities 

Applying IPA