What should you expect from your pathway analysis tools?
When it comes to data-driven science, your results are only as good as your data and your software. Whether free or premium, your choice of software will greatly impact your research and reputation, and you shouldn’t make it lightly. It’s not enough for a tool to be cheap – it also needs to do its job.
You might think that all a pathway analysis program needs to do is just that: analyze genes and proteins in the context of pathways. But you’re analyzing more than a simple collection of genes. You need the causal relationships that connect them, including activation, inhibition, downstream outcomes and upstream factors.
While the free price tag might be enticing, barebones pathway analysis tools can’t provide any depth beyond simple, non-directional relationships.
Is the basic package good enough? Let’s check out what premium gets you.
- Context
- At a basic level, a pathway establishes a relationship between two or more genes, proteins, or other entities that results in a predefined biological function. The most important part of this relationship is the causality: if all you know is that umbrellas and rain are seen together, you might believe that umbrellas cause the rain.
- But when a relationship is enriched with the full context, including directionality, you can distinguish cause from effect. That can mean all the difference when trying to understand mechanisms and drivers of disease or other research questions. A premium pathway analysis program can show you the full picture, so you never have to rely on just correlation.
- Networking
- We’re all familiar with the importance of networking at work, and it’s important for pathways too. Basic pathway analysis applications like DAVID are restricted to predefined pathways, cutting your target out of its network of related entities. They also treat all genes as if they were equal and ignore if they’re activated or inhibited. This makes it much harder to understand the gene interactions and outcomes in your area of interest. Imagine learning about the news just through the headlines.
- Working with the complete network of relationships, including direct, indirect, activated, inhibiting and more, gives you a better understanding of your data and lets you focus your research.
- Comparisons
- The most important part of science, aside from “writing it down”, is validation. Comparing and contrasting your data with others’ can validate your results and show you potential shortcomings. You can also discover new connections and biological processes or hidden relationships shared between entities.
- Researchers and reviewers want to know: How can you make sure that your result is really a unique insight? Has this phenomenon been seen before but not identified? You need an unbiased approach that provides deep context, so you can be confident in your findings.
Your pathway analysis program should empower you to extract the insights you need for publishing. While premium analysis programs might seem like just a shiny interface, they are much more powerful. They’re backed by an extensive human-curated knowledge base, allowing you to analyze and compare vast amounts of data from the comfort of a single platform.
QIAGEN Ingenuity Pathway Analysis (IPA) pays for itself by giving you the tools you need, instead of forcing you to find them on the internet (or build them from scratch). Plus, if you’re ever unsure of anything, IPA is supported by a team of PhD-level scientists who are ready to help out. IPA can perform a comprehensive set of over 20 unique analyses, which will help you:
- Predict pathway activation and molecular activity
- Understand regulatory networks
- Match your data analyses to patterns found in 200k+ curated datasets
- Explore expertly curated ‘omics data from 700k+ biological samples
When it comes to pathway analysis tools, the price reflects the value. Sometimes, you just need more.
