Sentence examples for pathways were taken from inspiring English sources
The steady state model equations and parameters relevant to cAMP-PKA and MAPK pathways were taken from our previous work.
Therefore, while investigating the association between cortisol and delirium, both traumatic stress-related and psychiatric pathways were taken into consideration.
Pathways were taken into account when P-values, after correction for multiple testing and resampling, were below 0.05 and genes with z-scores >1.96 were considered significant contributors to the pathways.
The definitions of DNA repair pathways were taken from KEGG database [ 2]. Figure 3 shows the difference between application of the standard organic layout for this small network of genetic interactions and PCA-based DDL (computed here without applying data matrix double-centering to take into account tendencies of genes to interact with smaller or larger number of other genes).
The pathways are taken from Reactome pathway database.
Users can also revise this default setting to a positive number when universal pathways are taken into consideration.
Genes/proteins molecular function, biological processes and cellular component is imported from the Gene Ontology project; while information on biochemical pathways is taken from KEGG.
The resulting 866 CP and 751 BP pathways are taken as candidate functional regions for our aggregated association analysis of Crohn's disease.
However, all the possible splitting and re-formations of carbon skeleton in the considered pathways are taken into account [ 30, 31].
Then, the lncRNA combinatorial effects in a given GO annotations or KEGG pathways are taken into account by the simultaneous analysis of multiple lncRNAs in user-selected individual or multiple datasets, which is realized by enrichment analysis.
Such prioritization is well developed in human disease genetics, where several criteria, such as the putative deleteriousness of a variant, evolutionary conservation, and known biological pathways, are taken into account [ 11- 23].
