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Is the overlapping phenotypical output the result of pathway modulations that are implemented sequentially (and thus likely in independent fashion) or concomitantly (and thus possibly in mutually interdependent fashion)?
In this approach we focus on transcriptional effects that can be linked to the phenotypic changes as a result of pathway blocking by ERK knockdown.
Phosphorylation of other residues (Thr, Ser and human cognates) is the result of pathway dependent ERK-linked activation of other serine threonine kinases.
One of the common result of pathway analysis using the various databases was the significant enrichment of elements of the innate immune system in low fertility samples (Table 1).
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The uncertainty is the result of pathway-dependent phosphorylation events in which ERK drives the activation of other kinases, since some of the proposed sites do not match the target motifs of MAPKs, and may also reflect cross-talk in which phosphorylation at one position exposes other positions to phosphorylation.
Therefore, the effects seen in animal studies may be completely or in part the result of pathways not important in humans.
This network provided a simple way to present the statistical results of pathway abundance and interpret the effects of the crt genes in a metabolic view, and the results highlighted the up-regulation of eight pathways and the down-regulation of three pathways in the lycopene fast production phase.
An alternative system with the potential to dramatically improve the results of pathway analysis has been recently proposed [21], which keeps track of the interdependence of genes.
In this study, we used Fisher's combined probability test to combine the results of pathway analysis in a large GWAS dataset and a smaller expression dataset.
The results of pathway level investigations of the marine bacterial extracts are summarized in Table 3.
Detailed results of pathway analyses are given in Table 2 source data 1.
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