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The 22 genes used for the hierarchical cluster analysis came from the adipogenesis human pathway [12] and literature review [13].
Human pathway databases, including Integrating Network Objects with Hierachies (INOH), Reactome, Kyoto Encyclopedia Genes and Genomes (KEGG), Biocarta, National Cancer Institute (NCI) and NetPath, were imported into the software for pathway over-representation of statistically significant genes.
Therefore, selecting only the subset of the genes annotated to KEGGs, a gene coexpression pair was considered a "true positive" when both genes of the pair were included in a common KEGG human pathway.
For databases of pathway/gene set network, Sudhir, et al. developed Human Pathway Database HPDD) to enable the study of human pathway networks [ 8].
Pathway analysis revealed seven significantly altered pathways in the WikiPathways human pathway collection.
This result is in accord with similar experiments done on human pathway databases [ 11].
Similar(21)
http://tanlab.ucdenver.edu/kMap/ Pathways Reactome Pathway database with visual representation for 21 organisms, which includes over 1500 human pathways.
In turn, this means that aquatic communities tend to be more different to each other, and thus that the increased rates of species movement caused by human pathways have large potential for impacts on biodiversity.
The objectives of this initiative, after the initial screening, are to prioritize chemicals for further investigation of toxic effects and progressively build toxicity models as well as develop assays that measure responses of human pathways towards these chemicals.
ALIGATOR enrichment analysis was also performed on 194 KEGG [20] human pathways.
We extracted the human pathways from MetaCyc; however, only one metabolic pathway was not included in HumanCyc.
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