The authors found functional modules of co-expressed genes for each developmental stage indicating sequential order of transcriptional changes in relevant pathways.
We identified modules of co-expressed genes in Cytoscape 2.5.1 [29] using the organic clustering algorithm.
Stimulation with pro-inflammatory cytokines or bacterial products may be expected to identify other modules of co-expressed genes.
A total of 507 modules of co-expression in cancer, defined as sets of genes co-expressing for a particular set of microarrays, were downloaded from L2L [22].
A total of 618 signatures (differentially expressed genes) from human microarray experimental results and 507 modules of co-expression in cancer were downloaded from L2L [22].
The LeMoNe algorithm, starting from an expression data matrix and a list of candidate regulators, will produce a module network, composed of modules of co-expressed genes and their associated regulators.
We have analysed 618 signatures and 507 modules of co-expression in cancer looking for significant values of four main protein-protein interaction (PPI) network parameters: connection degree, cluster coefficient, betweenness and number of components.
Such a computational approach, starting from expression data alone, can be helpful in the process of identifying the function of miRNAs by suggesting modules of co-expressed genes in which they play a regulatory role.
Most transcriptional modules of co-expressed genes were conserved.
WGCNA identified five modules of co-expressed genes.
We identified modules of co-expressed genes by applying K-means cluster analysis.
