There exist standard graph-based methods to search and eventually enumerate pathways in metabolic networks, but these methods including PathFinding [ 14- 16] and Pathway Hunter Tool [ 17] are computing pathways and shortest pathways in graphs instead of hypergraphs.
The pathway based gene expression similarity measuring methods, PEPC, we suggested here, compute pathway level expression by averaging expression of genes mapped to pathway.
We also computed "pathway perturbation scores," which were assigned the minimum AC50/LEC value for a chemical in any assay that was mapped to a gene in the pathway.
Lastly, we computed pathways from glucose to 5'-inosine monophosphate (IMP) to validate usefulness of the method in generation of alternative biochemically realistic pathways.
MESSI uses publicly available metabolomic data from characterized S. cerevisiae strains for computing metabolic pathway activities and ranks the strains based on user-defined pathways of interest (single or multiple pathways).
As was discussed in Section 2, the SNP parameters are treated as nuisance parameters and are integrated out of the analysis, for computing the pathway effects.
The mechanism of chloride transfer past the cis retinal is determined here by computing multiple pathways for this process.
In order to visually represent the relationship between the different KEGG pathways we computed a pathway similarity matrix based on the Jaccards Index of overlap.
Using gene set enrichment analysis, each sample was computed a pathway aberration profile that reflected its molecular state.
To visually represent the relationship between enriched KEGG pathways in the clinical dataset, we computed a pathway similarity matrix based on the Jaccards Index of overlap.
However, when these methods were used, a very small number of genes exceeded the threshold of significance, not enough to compute any pathway searches.
