In the following we describe popular competitive and self-contained pathway methods.
In Table 2 we show an overview of self-contained gene set and pathway methods that are describe in the following in more detail.
Clomburg et al. (2012) used a bottom-up strategy to reconstruct a functional reversal of the β-oxidation cycle for production of carboxylic acids through the assembly of well-defined and self-contained enzymes composing the pathway (Fig. 4a).
The school, run by Rosie Reynolds, says it offers "an inclusive child-focused environment with a strong Montessori pathway … in a self-contained old chapel, and offer an all inclusive open-door approach.
Pathway enrichment analyses used a self-contained gene set enrichment approach (16) using ULSs as compound "sets".
She contains multitudes, and remains self-contained.
A pathway-level analysis was conducted using the self-contained gene-set analysis method, GLOSSI [ 54].
Self-contained methods, in contrast to competitive methods, only consider results within a pathway or gene set of interest.
Further, a pathway-level analysis was conducted of all 378 genes using the self-contained gene-set analysis method GLOSSI.
In contrast, self-contained methods can be used for genome-wide studies as well as candidate gene or pathway studies.
