One way to establish the performance of a data analysis tool such as the Upstream Regulator Analysis in IPA is to validate the tool with published experimental examples of differentially expressed gene data and identified transcription factors and other upstream regulators.
This white paper has described several examples from the published literature where the identified regulatory molecules are among the top-scoring results in the IPA analysis. In addition, when such a tool can trace the signal cascade back to the stimulus or receptor, it is clearly producing relevant results. This validation is most clearly illustrated in the last example where IPA’s Upstream Analysis capability accurately identified TNF as the top-scoring molecule in cells exposed to that stimulus, revealing its importance in driving the signaling cascade.
IPA's Upstream Regulator Analysis Validation Whitepaper:
A Novel Approach to Predicting Upstream Regulators