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The Cell differentiation module is another example where different but related functions are observed together.
These results confirm our earlier finding that the signed black module is a pluripotency module while the signed blue is a differentiation module.
Module eigengene based connectivity enabled us to identify novel candidate genes in the differentiation module, like Uqcrh, that warrant experimental validation.
In the following we show that a pluripotency/self-renewal and a differentiation module can be found in this new data set.
Specifically, using signed weighted gene co-expression network analysis (WGCNA), we found a pluripotency module and a differentiation module, which are not identified in unsigned networks.
Specifically, we demonstrate that ER -tumours characterised by simultaneous high activation of a Th-1 differentiation module and low activation of a TGFB pathway module have better clinical outcome than tumours stratified by each pathway alone.
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By the same token, the same experiment could also repress differentiation modules to the exclusion of stemness modules detected in the negative list and therefore receive an extremely negative SE(Q−).
We also used Ingenuity Pathway Analysis, IPA, to compare functional enrichment in the pluripotency and differentiation modules (Ingenuity Systems, ).
Specifically, the black module can be considered a pluripotency/self-renewal module, while the blue, brown, and cyan modules can be considered differentiation modules in the signed network.
In our analysis, we found that different sets of regulatory elements were associated with this process in the CMCS cell and Cell differentiation modules.
The presence of the same function in different modules was also observed in the transcription regulation of degradative enzymes, which clustered in the Degradative enzymes and Cell differentiation modules.
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