Exact(3)
The result for different pathway numbers among these data sets is given in Figure 8.
The last column shows A. thaliana KEGG pathway numbers where the metabolite is predicted to be involved; all KEGG pathway numbers are hyper-linked to the corresponding KEGG website.
Enzymes/Genes numbering 1 to 7 from the cytoplasmic pathway, numbers 8 to 9 from the mitochondrial pathway.
Similar(57)
The first digit refers to the network category (metabolic pathway etc)., and the last four digits refer to the KEGG pathway number (if it existed in KEGG).
Pathway number 3, which has regulatory DC = 0.68 and co-membership DC = 0.005, is "Maturity onset diabetes of the young".
To reach one specific pathway in KEGG type in your web browser: " http://www.genome.jp/kegg-bin/show_pathway?ath0XXXX" being XXXX the pathway number.
The top 20 GO terms and KEGG pathways showing association with target genes were listed with GO terms, KEGG pathway, number of genes in the term, number of genes in the pathways, and P-value.
The top 20 GO terms and KEGG pathways showing significant association with target genes were listed with GO terms, KEGG pathway, number of genes in the terms, number of genes in the pathways, and P-value (Tables S5 and S6).
Pathway number 1, which has regulatory DC = 1.96 and co-membership DC = 0.12, is "Cell cycle" suggesting that the Cell cycle pathway does not tend to share genes, but to have regulatory relationship with other pathways.
Weak points: 5/ The significance of a disease-disease pair/link is tested by a permutation by random assignment of genes to pathways (albeit preserving number of genes in a pathway, number of pathways, etc).. Nevertheless, such a random assignment is valid only when one assumes as a null hypothesis that genes in a pathway are mutually independent of each other.
Pathway number 2, which has regulatory DC = 1.47 and co-membership DC = 0.39, is "Pathways in cancer" suggesting that Pathways in cancer shared high number of genes with several pathways and their genes also regulate the unique genes of other pathways.
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