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Thus evolution is perhaps not as random as is sometimes depicted, but will follow predefined pathways.
Neither of these methods requires predefined pathways, instead they explore the structure of the network freely.
These methods are based on integration of pathway topology with gene expression measurement to assign a statistical significance value to predefined pathways.
Inter-individual variances of gene expression among the different groups were analyzed using predefined pathways and functional categories annotated by KEGG [ 32].
Thus, the network-based analysis methods partially overcome the disadvantages of ORA, in terms of the limitation to the predefined pathways or gene sets.
Instead of redefining pathway boundaries based on an interaction network, this approach directly utilizes predefined pathways and thereby complements the search for activated or regulated genes and pathways by taking into account how they may interact.
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Methods 299 consecutive patients in the control group were compared with 427 patients directed into a predefined pathway.
KaPPa-View [ 22] and MapMan [ 23] display metabolite and transcript levels for predefined pathway blocks in plants.
KaPPa-View (Tokimatsu et al., 2005) and MapMan (Thimm et al., 2004) are plant-specific tools that display metabolite and transcript levels on predefined pathway blocks.
It subjects a list of interesting metabolites (e.g., differential metabolites) to statistical analysis to detect whether the given metabolite set is overrepresented in a predefined pathway.
While asking a question, the participants stated that it was easy to navigate through a predefined pathway to a single end-point: press button to send a question to an expert (see Additional file 3: TIFF file - Screenshot webpage Select expert(s) - Button to send question - Expert reaction time and appreciation).
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