Ingenuity Pathway Analysis (IPA)

Contributed by Poyin Chen

Scientific research is slowly but surely moving away from one gene-one organism focus. We now understand that individual genes are only a small part of a whole, just as a single organism is only a small part of a large, diverse community. The constant improvement in –omics technologies is creating a large influx of genomic, transcriptomic, and metabolomic data on community interactions.

With this influx comes the problem of how to make sense of these data in a biologically coherent manner. While knowing how one gene or one metabolite is changing in response to different treatments used to be satisfactory, knowing how this change is impacting up and downstream pathways is much more impactful and relevant in today’s research environment. Ingenuity Pathway Analysis (IPA), a software provided by Qiagen, draws together all known (published) knowledge on pathways in the human model. IPA is curated with all known pathways in humans, such as metabolic, inflammatory, and disease pathways.

What I find exciting is that IPA allows for simultaneous analysis of transcriptomic and metabolomics data sets. With this feature, I will be able to visualize infectious disease networks and their associated molecules to ascertain the impact of bacterial infections and preventative treatments on the host. Changes in gene expression levels may not always equate to an equivalent change in small molecules in the cell. Using IPA as as the interface between my transcriptomic and metabolomic data sets will help to further make sense of the puzzle that is life.

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