In the next step, modules of expression profiles, (i.e. sets of genes with high topological overlap) were formed based on hierarchical clustering, with empirically specified minimal module size (30 for gene expression, 10 for miRNA).
This shows that with the modular approach it is not only possible to discover "natural" modules of expression, but also to address questions about their evolutionary history since the divergence of two species.
Since the expression and methylation data were measured for the same set of samples, we are able to also provide the module membership of expression profiles in methylation modules and vice- versa.
The weak preservation of co-expression modules in methylation data and vice- versa shows that in general modules (clusters) of expression probes do not correspond to modules of methylation probes.
The aims of the current study are i) to relate expression levels to methylation levels, ii) to relate co-expression modules (clusters of expression probes) to co-methylation modules, iii) and to study the relationship between genetic markers, methylation and expression in whole blood of a relatively large (n=148) set of healthy human subjects.
The data revealed that at the apices of each module higher level of expression of myotrophin and EGF can be detected, while the base of each module is characterized by a high steady-state expression level of soluble frizzled molecule.
Among the genes found to be differentially expressed, we identified transcriptional modules of correlated expression across-tissues using the hopach package Hierarchical Ordererd Partitioning and Collapsing Hybrid; [ 61].
Our results show that a robust module network analysis of expression data can provide novel insights of miRNA function in important cellular processes.
Two association modules of mRNA expressions contain microRNA expressions as drivers.
We identify nineteen modules of gene expression reflecting multiple waves of transcriptional up- and down-regulation which characterize adipogenic differentiation.
