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Red bars represent the numbers of proteins in a given pathway that differentially expressed between groups.
This procedure was carried out separately for each disease and given pathway.
NTK is a measure of the degree that a given pathway differs from the other pathways.
The activity of a given pathway is then inferred by combining the log-likelihood ratios of the constituent genes.
In panels A, B and D, vertical bars represent the magnitude of the psc for a given pathway.
We also employed permutation analysis to examine if DEGs (p<0.01) are statistically significantly enriched in a given pathway.
In addition, the assumption of independence between gene expressions within a given pathway may not be valid.
The genes that were not included in these datasets were removed from the gene set for the given pathway.
Ingenuity calculates p-value for the probability of finding a set of genes within a given pathway.
We first approached this question by clustering the chemicals on the basis of their ability to modify the transcriptional activity of a given pathway.
Table 5 lists pathways using the second method, based on the standard deviation between differentially expressed genes in a given pathway (Top differentially-affected pathways).
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