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In addition, to determine if a pathway was significantly disrupted in the given cancer type, we further filtered the selected pathways that were ranked in the top 20% based on pathway activity scores in each cancer type.
Their similarity score is derived from pathway similarity based on pathway components (see reference for details).
Links between PTs are based on overlapping biological pathways (Section "Pathway-based human phenotype network").
Based on this integrative pathway analysis, we defined these 13 pathways as candidate pathways for prostate cancer.
Additionally, metabolites within specific KEGG pathways can be downloaded based on a KEGG pathway identifier.
Previously, pathway analysis methods had been developed based on algorithms considering pathways as simple gene lists and ignoring pathway structure.
Herein, we demonstrated metabolic state switching from the cell growth mode based on the metabolic pathways of the wild type strain to a GABA production mode based on a synthetic metabolic pathway in Escherichia coli through rewriting of the metabolic regulatory network and pathway engineering.
Based on the KEGG pathway assignment of the functionally annotated transcripts, five metabolic pathways for AsA biosynthesis were identified: animal-like pathway, myo-inositol pathway, L-gulose pathway, D-mannose/L-galactose pathway, and uronic acid pathway.
We evaluated the similarities between cancer types based on the affected pathways.
Evidences of a degradation mechanism based on two competitive pathways are discussed: photo-redox and β-scission pathways.
a Classification based on the inflow pathway(s).
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