Average occurrence density (or background) of the pathway-associated ESTs is calculated as the ratio between numbers of pathway-associated ESTs and all ESTs tested.
The re-annotation of Illumina probes was used to create a custom background of genes for the pathway enrichment analysis.
Since some genes of interest were obtained from the isogenic Exelixis collection [50], we chose to isogenize the genetic background of Imd pathway mutants by outcrossing them against the same isogenic Exelixis background strain (w1118) using the crossing scheme described in S1.
As CaZF enhanced growth of wild type yeast in presence of nonionic osmolyte, we wanted to test whether it can function in the background of HOG pathway mutants.
A caveat is that the effect may be dependent on the genetic background of the infecting strain and the "pathway" for DAP resistance [ 27].
High scores were associated with poor prognosis in each of the studies, and were also significant compared with a background of random pathway permutations.
The comparison against the genomic background highlighted that the upstream part of the pathway presents a lower number of events of population differentiation than what can be expected for a pathway of this size; so the differences observed may be due to a lower variability of this part, rather than differentiation of the downstream part.
The genetic background of jasmonate signaling pathway mutants had less effect on WRKY gene expression.
However, recent findings support the notion that Stat3 also possesses the capacity to impair cell proliferation and oncogenesis in a manner that depends on the signalling pathway and the genetic background of the target cells [45].
Average occurrence (or background level) of a pathway associated ESTs is the ratio between numbers of the pathway associated ESTs and all ESTs tested.
As described in the background section, if a vertex is in a pathway, it has to be drawn close to the other vertices of the pathway.
