Motivated by the success of network-based approaches, our multi-purpose pathway analysis aims to provide a limited set of candidate drugs both for drug repositioning and combination, that can be directly evaluated by the experts or combined with other methods.
For these purposes, pathway visualization approaches, that is, 'pathway maps' – such as those described for Epidermal Growth Factor Receptor (EGFR) [ 9], Toll-like receptor (TLR) [ 10, 11], retinoblastoma protein/E2F (Rb/E2F) [ 12], yeast [ 13], or mammalian target of rapamycin (mTOR) [ 14] – are better suited.
Another and more generic perspective on addressing global health issues was offered by one of our participants who sought the construction of fundamental multi-purpose pathways in microbial cells, which may serve as platforms that can be tailored to many kinds of applications, using advanced tools for computer-aided design of genetic circuits (Carothers [2013]).
For illustration purposes, pathways 1 of MCF7 (figure 8) and 1 and 2 of MCF10A are presented with genes of the highly significant pathways listed in Additional file 1.
For health promotion purposes, pathways to improved well-being have been distilled into five activities; connecting with people, being active, noticing of your environment, continued learning and giving to others (known as the five ways to well-being).
The purpose of pathway enrichment analysis is to identify pathways with a significant number of differentially expressed genes, and thereby connect those genes with corresponding functional feature, i.e. a pathway.
For this purpose the Pathway Studio software was used.
For this purpose, a pathway clustering analysis was performed for the node proteins of the PPI networks in Hep3B and MHCC97H cell lines.
Not only were we unable to assign the same fraction of assembled guinea pig microbiome reads to KO's, but these KO's were more often also not assigned by general purpose functional pathway databases (KEGG, metacyc, SEED).
As the World Dams Commission reports, "the debate about dams is a debate about the very meaning, purpose and pathways for achieving development".
Thus, this approach can provide insight into the purpose of a pathway (e.g., noisy switch vs rheostat) and can readily be applied to other signaling pathways.
