They can either, like Gale, follow the HE route – which includes extra, university-accredited modules – or follow the core pathway, which excludes the HE options.
Any unique variant that overlapped a gene was identified and the gene lists were used in Core pathway analysis (Ingenuity Systems, Redwood City, CA) to identify pathways and networks that were overrepresented in the filtered dataset.
In the past decade, tremendous progress has been made in our understanding of the molecular genetics of tocochromanol synthesis in plants and cyanobacteria, and all the biosynthetic genes of the core pathway have now been cloned and studied in detail.
During the past several years, mutant and transgenic approaches in model organisms, particularly in Arabidopsis thaliana and Synechocystis sp. PCC6803, have allowed the full complement of core pathway genes to be isolated and studied.
Despite the existence of this core pathway, its mutants have different effects on miRNA abundance and miRNA target abundance.
These 13 polypeptides are all components of the respiratory chain, the core pathway in oxidative phosphorylation, the activity of which is the primary function of mitochondria.
For the EGFR pathway, we considered two representations: a "core" pathway with 11 proteins (Biocarta) and an "expanded" pathway with 47 proteins (HPRD).
Models 3 and 4 used the protein sites in the EGFR pathway from two sources: a smaller core pathway protein set from BioCarta (www.biocarta.com) and a larger EGFR related protein interaction network from HPRD/NetPath [41].
Downregulation of these core pathway components suggests repression of the basal response to growth factors, an effect that appears to be amplified by upregulation of the Ras inhibitor, NF1 (⇑1.81) and the ERK1/2 inhibitor, PTPN5, (⇑1.59).
The module was identified for k = 30, but similar enrichments were seen in the pathways identified for k values between 25 and 10 (The core pathway dysregulated for k = 10 is highlighted in Figure 5).
Few have restricted the reconstruction on the core pathway, whereas others are including more information by adding more cross talks with the core pathway molecules.
