Of note however, the FEM modules clustered most closely with a cluster of biological pathways which included proliferation, B-MYB activation, p53 mutation, PIK3CA activation and stemness, supporting their association with a highly proliferative and poor-outcome ER+ breast cancer (Fig. 5).
In this regard, we identified a cluster of Toll pathway related protein interactions, and predicted the potential link between the Toll pathway, RNAi pathway and expression of heat shock proteins.
The identified components correspond to a cluster of frequently observed pathways that have a similar structure.
For this, we converted the pathway compendium into a set of connected components (SuperPaths), each being a limited-size cluster of pathways.
Using David Bioinformatics, we found a cluster of genes enriched among KEGG pathways, Gene Ontology terms, and the Uniprot tissues related to immunity and autoimmunity (Supplementary Information).
The final method independent of the resultant gene set finds cluster of pathways based on gene membership, GO ontology and protein-protein interactions.
Overall, this cluster of pathways suggest that immune signaling, particularly TNF-α signaling, are prime targets for repurposed drug treatment in GWI.
The bithorax complex in Drosophila melanogaster is a cluster of homeotic genes that specify developmental pathways for many of the body segments of the fly.
KEGG pathway mapping identified a cluster of genes involved in L-cysteine biosynthesis, an important precursor for glutathione.
Genetic interactions were enriched within the clusters of pathways by a factor of 5.5, confirming the organisation of our pathway network is biologically significant.
