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aReference shows association between a given pathway and the HER2+ subtype.
Therefore, the scores between a given pathway and the genes within that pathway, as well as the scores between the pathway and all other genes, were separately calculated the results were then evaluated using receiver operating characteristics (ROC) curves.
About 74% of the enriched pathways (enriched in at least one subtype) are known to be associated with breast cancer or cancers such as those shown in Table 3 and 4. aReference shows association between a given pathway and breast cancer or other cancers.
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A seminal paper analyzed data across studies and concluded that between-animal variability of a given pathway can exceed 2 orders of magnitude (Scannell et al. 2000).
Since the assumption of independence between genes within a given pathway may not be valid, we again use permutations to determine the empirical p-value of MTS for each pathway.
In addition, the assumption of independence between gene expressions within a given pathway may not be valid.
The P-value was measured to decide the likelihood that the association between focus genes and a given pathway was due to random chance.
In this test, the p-value was measured to decide the likelihood that the association between 179 genes and a given pathway was due to random chance.
This form of representation has high face validity as the relationship between two metabolites, in a given pathway, is governed by a single or series of enzymatic reactions that can be viewed as being represented by the correlation between the concentrations of the two metabolites.
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).
(ii) A right-tailed Fisher exact test p-value for the probability under the null hypothesis that the association between those metabolites found in a given pathway of our list with all those constitutive of the corresponding canonical metabolomics pathway is explained by chance alone (the null hypothesis being that the function/data set association is just random).
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CEO of Professional Science Editing for Scientists @ prosciediting.com