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Furthermore, this assumes that without gene expression data all core pathways are used equally (flux value = 1).
For example, as many as 12 core pathways are disrupted in the majority of pancreatic cancers through multiple somatic mutations [ 3].
The functions of genes in core pathways are highly conserved, but we observed many changes in which genes are involved in osmotic stress, peroxisome biogenesis, and autophagy.
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Finally, several published prognostic gene lists were analyzed for enrichment among the 304 GOBP and among the 36 core pathways, and using the hypergeometric distribution, significant overrepresentation of the core pathways was reported.
These genes, alongside other key genes of the core pathway, are assumed to be differentially regulated in different genetic backgrounds.
This concept has been instrumental in understanding pathways leading to cancer, where mutations in any component of a given equivalence group (also called a core pathway) are mutually exclusive and tend not to co-occur in the same tumour [ 41, 42 ].
The phylogeny and evolution of the chlorophyll biosynthesis core pathway were analyzed both at the gene and pathway level.
hh was first identified as a segment polarity gene in Drosophila and the core pathway was delineated by fly geneticists.
If the hypothesized core pathway is validated by experiments, or consistent with prior knowledge, the association with the core pathway can prioritize the driver mutation.
By comparison to genome-wide ChIP-Seq data sets, we observe that this core pathway is enriched in genes under NF-κB/RelA control.
Thus, the core pathway is a good candidate for regulating polarised E-cad endocytosis during cell intercalation in contexts such as the tracheal system.
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