The mucin type O-glycan biosynthesis was found to be the most significantly enriched KEGG pathway using pathway union (Table 2).
In order to increase the stringency of the target pathway prediction, a posteriori approach (pathway union) was also applied resulting in the enrichment of the KEGG gene ontology terms mucin type O-glycan biosynthesis, ECM-receptor interactions, glycosaminoglycan biosynthesis (chondroitin sulphate), TGF- β signaling, and endocytosis (Table 3, Supplement 2).
For simplicity, with all data sets, we chose the 20 most up- and 20 most down-regulated (enriched) pathways, whose union formed a set of 40 classifying pathways, representing approximately 20% of all pathways used.
This sequence of neighboring points is referred to as a pathway, and the union of pathways forms a path through the index set.
We then took the 154 union pathways as candidate pathways of the three diseases.
Intersection yields the smallest number of mapped pathways, 190, while "union" group yielded 244 gene sets.
The provided canonical pathway consists of a union of the known signaling pathways responding to the following ligands TNFα, IL1α, IGF-1, and TGFα (see the Methods section for detailed description).
In such cases, two overlapped mentions (one gene/protein mention and one pathway mention) are merged into one pathway mention by using the union of text boundaries.
The existing global networks of functional coupling, such as FunCoup, PPI networks, the union of KEGG pathways, and so on, are known to be of high quality and relevance when applied to statistically evaluate functional relations between larger gene sets.
However, they are focused on the union of various (pathway) databases instead of explicitly pointing out the differences between pathway databases.
