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We next examined modules that are conserved among all species in our analysis, and 33 such groups were found, spanning various functional categories like signal transduction, protein folding, metabolic processes and many others.
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Open image in new window Fig. 1 The examined module of LS-2 PTC.
Every module began with a competitive session during Week 1. Weeks 2 through 4 were composed of small-group discussions examining module subtopics in greater depth.
By examining module articles in a stepwise manner, we develop a "lab meeting" atmosphere in the class, with experimental findings discussed as if they had been generated gradually by the students themselves.
To compare the performances of unsigned and signed WGCNA in identifying gene groups that are important for the regulation of the pluripotent state, we defined gene modules in unsigned and signed networks and assessed module function and importance by determining gene ontology terms associated with each module and examining module membership of genes known to play a role in ES cells.
Motivated by the same rationale that genetic variation that is associated with both the trait and gene expression is more likely to be biologically relevant than variants associated with the trait only, we mapped GWAS loci to CD4+ coexpression modules and examined the modules that were tagged by GWAS loci.
We examined one module, module 17, in detail because we are interested in stress responses, as module 17 was found to be enriched with GO terms relating to environment stresses.
Specifically, we examined DetMod modules and control (artificial and MCL) modules to see in which case the p-values were better.
Then, we examined these modules by validation criteria, which in turn substantiate that our subnetworks deserve the characterization 'functional module'.
Some examined course modules separately, others all in one go.
We only examined the modules with at least 10 genes.
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