This result suggests that the association between obesity and T2D depends on the coactivated gene clusters or pathways rather than a few individual disease genes.
For example, gene set enrichment analysis or pathway enrichment analysis [ 11- 13] uses the membership information in functional gene clusters or pathways, which facilitates an understanding of the underlying biological mechanism(s).
The analysis software tool GeneTrail [ 10] can be used for comparative analysis of transcriptome data to identify functional clusters or pathways rather than single genes that are affected in one experimental condition compared to another.
Further, when data from multiple genes that are known to be coexpressed in a cluster or cellular pathway are correlated, the result has greater significance than data from a single gene.
No functional annotation clusters or KEGG pathways were enriched.
Systems biology methods like ours are in high demand as the differences between many conditions, be they neurodegenerative diseases, brain diseases, different kinds of cancers, different degrees of disease severity, etc., are very subtle and cannot be easily highlighted using the usual off-the-shelf clustering or biological pathways identification algorithms.
By the tests, uncertain information can be omitted from further investigations, such as clustering, principal component analysis or pathway analyses.
These included results of cluster analyses, principle component analyses or pathway analyses.
GIs linking pathways from different clusters or involving unclustered pathways were recorded as uncharacterised.
Computational modeling and experiments suggest that the role of the iron-sulfur cluster biosynthesis pathway in infection is indirect, via competitive binding of the shared sulfur donor IscS.
