Advanced options
Pathway expansion criteria
A candidate node is accepted as a pathway expansion when it is strongly
associated with the pathway nodes and increases the pathway compactness.
On of the following three criteria have to be met:
-
association threshold - a minimum ratio of interactions between
the candidate node and the pathway vs interactions between the candidate
and the rest of the network
-
coverage threshold - a minimum ratio of pathway members connected
to the candidate node
-
triangle threshold - a minimum ratio of triangles between
candidate node, a member of the pathway and another node connected
to the pathway vs all such possible triangles
The thresholds can be set in the advanced options of the enrichment analysis.
To obtain more significant (but smaller) expansion, increase the thresholds.
To obtain larger expansion, decrease them.