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These findings suggest that the mechanisms involved in period2 regulation might represent a more general pathway leading to light induced gene expression.
Compared with other more general pathway approaches such as KEGG, the networks we describe contain edges that have one or more detailed evidences supported by a specific literature reference and contain tissue and species-level metadata.
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Among more general pathways (protein ubiquitination pathway, mitochondrial pathway), many pathways were related to the immune system (T cell activation, B cell activation) indicating the immune-specificity of the starting cells.
We propose that acquisition of lysozyme provides broad-spectrum protection against a subset of bacteria (e.g. Gram-positive bacteria) facilitating loss of more general pathways that respond to all bacteria (e.g. IMD).
However, in each category the more general KEGG pathway "Pathways in cancer" (hsa05200) enriched with genes forming the gene sets.
The cell possesses organelle-specific turnover pathways in addition to the more general autophagy pathway.
The first steps are part of the more general phenylpropanoid pathway including synthesis of soluble phenolics such as flavonoids and sinapic esters.
In this section, we recall the end-product module example (of which the simple ATP metabolism example is a special case) to analyse gene-expression regulation in a more general metabolic pathway.
However, when combined there is little evidence from this analysis to suggest that the signatures are capturing chemotherapy-specific mechanisms in addition to more general survival pathways.
The same considerations may hold for more general protein pathways where hub-like proteins ([ 34, 35]) are usually essential ([ 36- 38]) in the network and maintain sparse links between different modules, while other protein regulators characterize modules of smaller size.
Beyond the set of virulence genes analyzed so far are part of the best-known players in pathogenic phenotypes, the presence, absence or enrichment in other kind of virulence-associated or virulence lifestyle genes (typically coding for more general metabolic pathways) may be directly implied in pathogenicity (Wassenaar and Gaastra 2001).
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