Third-generation methods move beyond treating pathways as lists of genes, adding information about the connectivity and directionality of interactions.
Adjusted mean hospital LOS was significantly shorter for patients treated with pathway vs. non-pathway therapies (3.9 vs. 5.0 days, p < 0.01).
Finally, this study specifically compares those patients who were initially treated with pathway versus non-pathway antibiotics; therefore, other aspects of treatment, such as time to switch therapy, duration of treatment, and compliance may have unknowingly influenced outcomes.
Mean hospital LOS (4.9 vs. 6.0 days, p < 0.01) and total hospital costs ($3,184 vs. $4,168, p < 0.01) were significantly less for patients treated with pathway vs. non-pathway therapies; however, total pharmacy costs ($528 vs. $611, p = 0.12) were similar.
Secondly, through bioinformatic analysis of the predicted targets and of genes known to have altered expression in bleomycin treated mice, pathways through which the microRNAs could affect lung disease were revealed.
This represents a potential difference of 9 lives saved, 287 hospital days saved, and $228,452 saved if all of the 287 patients in the non-pathway group had been treated with pathway antibiotics.
Common approaches to pathway analysis treat pathways merely as lists of genes disregarding their topological structures, that is, ignoring the genes' interactions on which a pathway's cellular function depends.
We treated each pathway as a set, used GSEA's default configuration and applied its suggested criterion false discovery rate (FDR) to discover enriched pathways.
We also observed a decrease in hospital LOS and total hospital costs in CAP patients treated with pathway antibiotics, despite similar total pharmacy costs.
