Sentence examples for pathways as defined from inspiring English sources
The pathways identified by performing tractography through the ROIs were compared with known anatomical pathways as defined in human gross anatomy texts [30] and in connectional studies in experimental animals [31] [33].
The Database for Annotation, Visualization and Integrated Discovery (DAVID, available on http://david.abcc.ncifcrf.gov/) was used to interpret the lists of differentially expressed probes and to identify statistically overrepresented biological function categories of Gene Ontology (GO) and biological pathways, as defined in the Kyoto Encyclopedia of Genes and Genomes (KEGG).
First, using the gene set expression comparison tool, 302 pathways (as defined by Biocarta) were analyzed.
To this end, we mapped reactions in many different FCSs onto biochemical pathways, as defined by standardized annotations [ 41, 59].
Twenty pathways (as defined by KEGG, level 3) were found to be differentially abundant between the tumor and normal tissue.
However, gene set analysis in ConsensusPathDB is only allowed for pathways as defined by the original sources.
The hypergeometric probability test was used to calculate the probability of finding at least the observed number of metabolites of a given pre-defined metabolic pathway (as defined on the KEGG pathway database) in the clusters identified through the GSVD algorithm, with knowledge of the total number of metabolites present in that pathway detected by LC-MS in these samples.
For example, GSEA found that the strongest perturbation is observed in a set of 47 genes defining a CIRCADIAN_EXERCISE pathway as defined in the MSigDB (Subramanian et al., 2005).
Using a compendium of microarray gene expression data from the M3D database [30], networks were constructed for the 27 genes contained in the ROS pathway as defined by the EcoCyc database [1] (Figure 2).
Using a compendium of microarray gene expression data obtained from Escherichia coli, we constructed a series of Bayesian network models for the reactive oxygen species (ROS) pathway as defined by EcoCyc.
Genes coding for cell-cycle processes were also significantly enriched (P=0.0003) as well as the genes coding for chronic myeloid leukaemia pathway as defined by KEGG (P=0.04).
