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The second equation above defines f'l to be the relative frequency of the module genes present in any SGLs of type l.
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To visualize the tissue specificity of the expression modules, the activity profile of each expression module was calculated by taking a mean of the expression profiles of the module genes, and presented as a heat map (Figure 8).
These modules overlap with 16 genes present in at least 3 of the 4 modules including Ccrn4l, Gadd45g, and Map3k6.
The Netpath (1.1.2015) [ 24] Androgen Receptor (AR) pathway was representative of the genes present in module 8.
Another example of a pathway that is overrepresented amongst the genes present in modules SAT 4 and SAT 8 is the Toll-like receptor signalling pathway.
From the set of significant co-occurrence modules, a co-occurrence network was constructed in the following fashion: For each module, the gene names are represented by vertices and an edge is drawn between all pair-wise combinations of genes present in the module.
genes from each module were compared to databases of genes present in specific cellular pathways and processes.
The enrichment for this transcription factor motif in the genes present in this module is consistent with a dual functional role for NRF1 in potentially balancing myogenesis and mitochondria production with energy dependent protein catabolism.
For the purposes of illustration, the co-expression profiles of the genes present in the neuron module, plus that of TLX3 [38] (which was not a member of the PCIT-driven module, but was identified by the Module-to-Regulator analysis) are shown in Figure 6 using the 26 treatments of the Overall landscape.
All genes present in those modules are presented in Additional file 1.
The genes present in these modules are listed in Additional File 1.
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