We used a hypergeometric test to identify gene sets from the MSigDB [19] that are over-represented in the molecular paths detected by the EMPath method.
The molecular paths coupled cellular components and processes distant at first sight but associated through different biochemical interactions with the oxygen-dependent phenotype changes in S. cerevisiae.
In this sense, pathway-based approaches provide a complementary role to single-point analysis for interpreting the molecular paths underlying human diseases.
The Au Au interaction induces a twist in the molecular structure that is responsible for a significant decrease in the conjugation path.
They were linked to the ACS1 encoded acetyl-CoA synthetase which was observed in the enriched molecular paths when the path detection was run solely with the transcription data.
As a result, we selected the genes found in the significant molecular paths (Figure 2) and visualized their differential expression across multiple studies available in T1Dbase (Figures S6 S9).
In addition to the respirative metabolism, fatty acid beta oxidation was observed in the detected molecular paths.
Interestingly, a number of transports between the cytosolic and mitochondrial compartments were observed in the detected molecular paths.
In addition, the methylisocitrate lyase reaction catalyzed by an enzyme encoded by ICL2, which is homologous to ICL1, was also included in the detected molecular paths.
This decrease is due to a decrease in clustering accompanied by a smaller effect (an increase or a decrease) in the path length.
Finally, by using the function phyper of the R stats package [40] we tested for enrichment of each gene set in each molecular path.
