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TNFNetPathRef (TNF NetPath pathway reference gene set), 184 genes.
KEGG was employed as a pathway reference database [ 19, 20].
Just as AlzGene for risk-gene reference database, AlzPathway serves as a pathway "reference" integrating wealth of pathway information published before.
Our AlzPathway provides a powerful AD pathway map for deciphering pathogenesis of AD, and it serves as a pathway reference database just as AlzGene for risk-gene reference database.
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Description of a technology; Number of patents registered for that technology; Number of scientific publications devoted to the technology; Technological alternatives or "projections" in gaining a technology with a short description thereof; Information about compatibility with other sub-technologies in a pathway; References and sources used for a profile.
Furthermore, for the metabolic translations, all nodes that do not correspond to physical instances of compounds or gene products were removed (i.e., pathway-reference nodes).
This analysis provides evidence for broad coordination of genes involved in EMT- and cancer-related pathways through chromatin remodeling (pathways referenced in this section are listed in Table 2, [all enriched pathways are in Additional file 12: Table S8]).
In contrast, nerve-related genes similarly down-regulated by femoral fracture at all three ages were broadly related to the nerve growth cone or to synaptic signaling pathways (references cited in Table 2).
These signaling intermediates were selected on the basis that they collectively represented a diverse set of known canonical signaling pathways (References mentioned in Additional File 1: Supplemental Table S1).
For example, we manually modified 64 mammalian-specific metabolic pathways from the reference pathways in MetaCyc and 2 pathways (Ketogenesis and Ketone degradation) that are important in lipid metabolism of mammals [ 73] were added [see Additional file 2].
TNFPathDBRef (TNF pathway database reference gene set), 63 genes.
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