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The module eigengene can be considered a weighted average of the module gene expression profiles.
These sequences might be putative operators for the binding of CI repressor which have been reported as regulators in the lysogeny module gene expression [ 20].
In order to relate module gene expression to clinical parameters and breast cancer subgroups, a rank-based module activity score [ 24] was calculated for each of the eight modules in each breast cancer sample.
While a common regulator for these three 'black' module genes has not been identified, the limited literature available points towards cytokines such as IL-2 (Interleukin 2) and IL-6 in the up-regulation of 'black' module gene expression, possibly through the activation of STAT proteins [ 30, 32- 34].
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The TPH2 SNP was associated with severity (p-value = 0.010) and moderately associated with the blue module gene expressions (p-value = 0.077).
Furthermore, we could show experimentally that a miRNA, assigned as the best regulator, is indeed a key regulator for the module genes expression.
In this module, we observe again a clear positive correlation pattern between miR-200a and the module genes expression, suggesting an indirect regulatory circuit between miR-200a and module 25 genes (Figure 2c and Figure 3a and 3b).
The results presented here showed that in general, each pathway responded as a separate module, with gene expression changes and enzymatic activities responding as a group.
Spleen module SP1 gene expression (1,234 genes, supplementary fig. S5, Supplementary Material online) was negatively correlated with Bd load (r = −0.72, P = 0.020).
A clustering method designed to elicit transcriptional modules from gene expression profiles, modulated modularity clustering (MMC; [51]), was used to construct putative transcriptional modules from the remaining transcripts associated with retinue response.
C. Genes from both Th17 SE module and Th17 gene expression module have lower expression when missing the transcription factors Stat3, Irf4, and C-maf.
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