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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.
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.
To use pathway-based markers in classification, we need a way to infer the activity of a given pathway based on the expression levels of the constituent genes.
(3) Calculation of an enrichment score (ES) for a pathway based on the gene-level test statistics.
First we aimed at identifying active signalling pathways based on the expression level of transcriptional regulators.
Pathways: counts for HumanCyc and Reactome are based on the lowest level of their pathway hierarchy.
Evidences of a degradation mechanism based on two competitive pathways are discussed: photo-redox and β-scission pathways.
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