Survey of Ingenuity pathway analysis

Overview

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IPA is software that helps researchers model, analyze, and understand the complex biological and chemical systems at the core of life science research. IPA has been broadly adopted by the life science research community and cited in hundreds of peer-reviewed journal articles.
Description: Ingenuity Pathways Analysis (IPA) is an all-in-one software application that enables researchers to model, analyze, and understand the complex biological and chemical systems at the core of life science research. IPA has been broadly adopted by the life sciences research community and cited in hundreds of peer-reviewed journal articles.
The  too is commercial

Advantages: straightforward and user friendly pathway visualization and analysis tool. Extensive help files are available. Metabolomics data can be uploaded as KEGG and PubChem ID. Every metabolite has its own ‘chem view’ page, summarizing chemical information, but also biological information such as ‘what does the metabolite regulate’, ‘by what is the metabolite regulated’, ‘what is its role in the cell’, ‘what does it bind’, and ‘what diseases are associated with the metabolite’. This biological information is created by textmining tools. References and citations of the information behind these biological associations are easily accessible. The tool creates on the basis of the textmining information and pathways biological networks of your uploaded metabolites (on the basis of the default algorithm ‘shortest path’).

Drawbacks: the information gathered by textmining tools are not manually curated by IPA, so you need to this by yourself and therefore be very careful in the interpretation of your results! There are no possibilities to visualize and analyze different datatypes (i.e. metabolite data combined with transcriptomics data). No possibilities to visualize & analyze your data on the level of biofluids such as blood and/or urine. Not species specific. No possibilities to edit own pathways or networks.