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For each pathway, proven technologies are presented and their advantages and drawbacks are described.
This generated matrixes of p-values and odds ratios for each pathway and from each direction.
For each pathway a z-score was computed as previously described [2].
The next step was to calculate psc values for each pathway using their corresponding L-values.
To compute a P value for each pathway, IPA implements Fisher's exact test.
For each pathway, P-values were corrected for multiple comparisons (q-values) using the false discovery rate[52].
For each pathway psc value, P values were calculated to estimate the statistical significance of these scores.
That is, for each pathway, and according to (2.4), we listed the genes which are members of the pathway.
The most significantly regulated genes are listed in File S1 for each pathway regulated by each compound.
The rates for each αi are specified, as shown in presented in Table 1 for each pathway.
The FDR is provided for each pathway.
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