Alternative to the steady-state method: derivation of reaction rates from first-passage times and pathway probabilities.
Our GSEA of this dataset identified statistically significant altered pathways, as follows: (1) calcium-dependent cell-cell adhesion pathway (GO 0016339), probability of 73%; (2) protein digestion and absorption (KO 04974), probability of 66%; and (3) negative regulation of synaptic transmission, glutamatergic (GO 0051967), probability of 55% (Table 6 and Figure 4).
In other words, among all the genes, PIAS2 would the most likely cause the ESC-to-EB transition of the pathway behavior (probability 0.0035 in human and 0.014 in mouse) when its initial transcription state of up-regulation in ESCs is altered to down-regulation (Table S3).
As expected, in the paired pathway, the probability of AP firing by EPSP trains was significantly increased 10 and 20 min after conditioning stimulation (Figure 8C and E; "LTP group Synapse I", pre = 0.69±0.17, 10 min = 2.84±0.40, n = 9, p = 0.013 compared with "noLTP group", n = 5).
For each pathway, the probability values were computed based on a modified Fisher exact test.
For each pathway, the probability of involvement of the respective number of PDGFC-associated genes was expressed as a P value; values of 0.05 were taken to be significant.
If an invasive species is regularly transported along multiple pathways, the probability of its successful establishment is increased (Kolar and Lodge 2001).
However, given that we have noted corresponding differences in fold change, GSEA predictions and pathway signature probabilities, it is likely that this is a reflection of the number of samples used in the analysis.
We can quantify a particle's mean (average) lifetime, its possible decay pathways, the probabilities associated with each one, etc.
