Exact(2)
A subtler test of pathway independence is to ask if two pathways are kinetically correlated in individual cells.
For these reasons, we opted not to perform a traditional test of pathway or gene ontology enrichment for sets of GxE genes, for example for all GxEs affecting triglycerides (TG) or all GxEs pertaining to SFA intake or even all TG-SFA GxEs, but to examine the GxE gene function in the context of metabolic syndrome (MetS).
Similar(58)
The remaining group was used as the true normal set for the test of pathway-based identification of cancer.
Therefore, different gene measures have their adaptive tests of pathway associations: 2ndP and fishP are more fitting for a gene containing multiple SNP effects, while minP and simP are more suitable for a gene having extreme SNP effects.
We implemented two conservative measures to the serial significance testing of pathways for enrichment.
None of these pathways survived correction for multiple testing of pathways at a false discovery rate of less than 0.05 (all q-values were >0.15).
The differentially expressed unigenes (DEGs) between any two libraries (PIP vs. HP and PIP-60 vs. PIP) were calculated according to the method by Audic [ 50], a hypergeometric test of GO and KEGG pathway enrichment was performed.
Increased grassland arthropod production with mammalian herbivory and eutrophication: a test of mediation pathways.
The method provides a lateralising test of vestibulospinal pathways for balance.
To test the utility of pathway CV estimates for interpreting metabolic pathway response to experimental variation, I investigated the response datasets.
In addition to org.Rn.eg.db (2.2.11), the bioconductor packages including KEGG.db (2.2.11), and GOstats (2.10.0) were used to obtain the gene to pathway mappings, and to test the significance of pathway enrichments.
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