Sentence examples for pathways were computed from inspiring English sources
To directly assess the relationship between correlation network structure and metabolic pathways, average shortest paths in the metabolic pathways were computed for the members of each network component and for each module.
For each of the randomly composed datasets, the numbers of conjoint pathways were computed.
Pathways were computed from each molecule to every other molecule in the query set.
Extreme pathways were computed by using the Mac OSX version of the ExPA program [ 6].
Some plant-specific pathways were computed repeat by extracting genes from comparing Pst with Bgt stress.
A KEGG enrichment analysis was then performed for each list as described above, and the common pathways were computed.
Finally, a functional similarity score (funSim) between two pathways was computed via cosine measure.
The pathways were ranked within each method and the fraction of real versus total pathways was computed and visualized.
In our methods the optimal pathways are computed in a post process by ranking the pathways that have been enumerated.
After P-values for all pathways are computed, FDR is calculated to correct for multiple testing with FDR = P*m/k, where m is the total number of pathways and k is the rank of the pathway under consideration.
For each element, the number of inputs received from other pathways was computed as the number of arcs connecting an upstream (in the tail of the arc) IT pathway protein with a downstream (head) non-IT pathway protein; conversely, the number of outputs was computed as the number of interactions between a downstream IT pathway protein and an upstream non-IT pathway protein.
