You might think that spending thousands of dollars to meet your bioinformatics needs guarantees the most accurate analysis on the market. Well, it’s actually a lot more complicated than that! Expensive pathway analysis tools such as Qiagen’s Ingenuity Pathway Analysis (IPA) don’t necessarily give you the results you need. In fact, they make you spend extra money up front and waste your time by forcing you to sift through poorly-targeted results. Fortunately, iPathwayGuide has you covered on more than just price. Here is a brief comparison between iPathwayGuide and Ingenuity Pathway Analysis.

The true difference comes down to three key components: power, flexibility, and cost-effectiveness.

Comparison between capabilties and value provided by iPathwayGuide vs. Ingenuity Pathway Analysis (IPA)

iPathwayGuide provides a more powerful analysis yielding better quality results at a lower cost compared to Ingenuity Pathway Analysis (IPA)


  • Ingenuity Pathway Analysis shows you the haystack.
    In Ingenuity Pathway Analysis you can spend hours sifting through piles of results, and still not be confident that you’ve found the right answer. Why is this you might wonder? This is because Ingenuity Pathway Analysis uses an enrichment analysis that usually yields lots of false positives and also is unable to identify all true positives. Here is a blog which shows the results of the enrichment analysis in a case when the truly impacted pathways are known.
  • iPathwayGuide helps you to quickly find the needle in the haystack. Why would iPathwayGuide do better than IPA you might wonder? This is because iPathwayGuide uses a sophisticated impact analysis that has been shown to eliminate most false positives, as well as identify much more of the true positives. Here is a side-by-side comparison of the results of the impact analysis vs. the old enrichment analysis. The impact analysis is also well-recognized and widely cited. Here are some details about the science behind it, and the landmark papers that introduced the concept of topological analysis.


  • Ingenuity Pathway Analysis locks you down.
    With Ingenuity Pathway Analysis you may be restricted by limits on the number of users who can be logged in concurrently, or even relegated to one machine. Also, you cannot share the results of your analysis with somebody who does not have a license.
  • Access iPathwayGuide from anywhere, anytime, regardless of who else is logged in. We also encourage open sharing of results without additional subscription requirements—after all, it’s your data.


  • Ingenuity Pathway Analysis will nickel and dime you for every feature.
  • iPathwayGuide is all-inclusive.
    Our customers tell us they switched to us because they get much more value at a more competitive price.

Whether you’re an individual lab looking to analyze your research data, a core facility/ service provider, or you need institution-wide coverage, our packages are designed so that you pay for what you need, and not what you don’t.

Contact us to learn about our flexible pricing options.


But what about the quality of the analysis? Am I going to be satisfied? Don’t I get what I pay for?

Here is why our dynamic, interactive cloud-based report is so powerful.

Accuracy: the best algorithms = clearer results. Higher confidence.

  • iPathwayGuide’s pathway ranking algorithm is used by 9 of the top 10 pharma companies because they recognize it as “state of the art.”
  • We’ve integrated advanced algorithms into our gene ontology analysis so that you can find the terms that are both significant and specific, allowing you to get at the actual biology that’s underlying your experiment.

Quality: a well-designed UI means life scientists stay engaged in their own analysis.

  • The interactive experience is designed to highlight results and evidence, while encouraging exploration.
  • Compare results across several experiments: time points, tissue types, doses, patient subgroups, and much more using our one-of-a-kind visual, interactive Meta-Analysis.
    • This feature is especially effective for multi-omics data

Convenience: we work for you, not the other way around.

  • No restrictions on the number of concurrent users.
  • No restrictions on physical location, IP address, or specific machines.
  • Share your results (1 click) with anyone (no subscription required).
  • Print an auto-generated Executive Summary for any analysis.


Are you ready to jump in? Register for a free account to check out the demos. Or, contact us with your questions.