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Importantly, genomic pathway cluster designation remained within the model as an important predictor of clinical outcome (cluster 1 vs. cluster 4; HR 4.31, p = 0.18) (Table 1).
Drugs targeting a common pathway cluster together even when they inhibit different proteins and the approach has been used successfully to study the mechanism of action of compounds [31], [32].
A KEGG pathway cluster was conducted using common perl scripts.
We show that the GAL pathway cluster is conserved in all Candida species present in CGOB.
In the biochemical pathway cluster, CXCR4 was a gene of interest.
Pathway cluster P9 is distinguished as commonly upregulated in tumor samples.
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Here we summarize the main pathway clusters activated by PHEO- and PGL-susceptibility genes: pseudohypoxic, kinase, and Wnt signaling.
Pathway clustering identified genes of the immune system including inflammatory signaling, and components of the complement cascade upregulated during vasoregression.
Finally, chemotherapy sensitivity patterns were assessed across groups of patients defined by both pathway clusters and age (≤45 years and ≥65 years).
Multivariate modeling evaluating classification of breast tumors arising in older women by oncogenic pathway clustering and important clinico-pathologic variables was additionally performed.
Additional parametric analysis to generate gene ontology (GO) term clusters and KEGG (Kyoto Encyclopedia of Genes and Genomes: http://www.genome.jp/kegg/) pathway clustering was performed using WebGesalt algorithms (http://bioinfo.vanderbilt.edu/webgestalt/).edu/webgestalt/
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