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. 2014 Aug 21;42(16):10288–10306. doi: 10.1093/nar/gku722

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© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 5. — Six variants of MIPA approach. In Variants 1–3 (panels A, B, C), competitive tests evaluate all five measures, just like self-contained tests. Variants 4–6 (panels D, E, F) use a single t-test between the distribution of pathway activity measures observed per sample in the given dataset and that in randomized gene sets. Variants 1 and 4 (panels A, D) combine P-values using Stouffer's Z-score method and then use the larger value of the two as the final P-value for a pathway. Variants 2 and 5 (panels B, E) directly combine the P-values from all tests into a single overall value using Stouffer's Z-score method. Variants 3 and 6 (panels C, F) assign the largest P-value as the final value for a pathway.