Signaling pathways are often used to regulate transcription factors to specify the genes for active transcription.
Given the fact that some genes specifically cooperate to take over some highly specialized cellular functions, pathways are often used to represent part of the gene-network at a more detailed level.
The yeast MAPK signal transduction pathways are often used to test the effectiveness of the pathway inference algorithms [ 5, 7- 9].
The environmental exposure pathway framework is often used to describe associations between pollutant sources and health effects via emissions, environmental concentrations of pollutants, pollutant exposure pathways (e.g., mouth, nose, ears, eyes, skin), and dose (i.e., micrograms of pollutant ingested per day) (Agency for Toxic Substances and Disease Registry 2005).
This is a breeding value computed from the individuals sire, maternal grandsire, and maternal grand sire breeding values from 2003, before the bulls in the validation data sets had any daughter information (this "sire pathway" breeding value is often used for selection because dam information may be missing or biased).
In these cases, strong enrichment in plausible Gene Ontology categories or detection of known pathways or annotations is often used to demonstrate utility, as in [ 19- 25].
Thapsigargin, which inhibits SERCA and thereby causes loss of Ca2+ from the ER without engaging the signaling pathways used by receptors, is often used to activate SOCE.
In order to understand the mechanisms behind this sensitisation process we have used anisomycin, an agonist of the JNK pathway in mammalian cells, which is often used in studies involving JNK because of its specificity and potency in activating the JNK pathway.
The drug avoids a major metabolic pathway in the liver that is often used by other drugs, but it does not completely avoid being metabolized by the liver.
Chassagnole et al. (2002) constructed an integrated ODE model of glycolysis and PP pathways [ 12, 28], which is often used as a base model in many studies [ 26, 27, 29, 30].
P pili are assembled on the bacterial outer membrane (OM) via the chaperone/usher (CU) pathway (Thanassi et al., 1998), which is often used as a model system to elucidate the mechanism of pilus biogenesis (Waksman and Hultgren, 2009).
