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Figure 10 Internal structure of a node composite module in the Castalia simulator.
Modules can be combined together in any order, but are cloned sequentially one module at a time to form a composite module, which can then be further subcloned.
Overrepresentation of TF-binding sites and composite elements (TF site pairs) were computed by the F-Match algorithm and composite module analyst program (Composite Module Analysts) that is implemented in the geneXplain platform (www.genexplain.com).
The permutation test of the modulePreservation function leads to a composite module preservation statistic referred to as Zsummary.
We further identified combinations of binding sites of enriched transcription factors that correlate with coregulation of inflammatory but not of control genes by using the composite module analysis tool http://www.biobase.de.de
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Composite materials are a key element in weight reduction strategies, so the analysis of the mechanical behavior of assemblies of composite modules is of great importance.
Moreover, an enrichment of defined composite modules has been observed in selected auxin-related gene families.
Specific ZRE, MRE/MYC2 and AuxRE-related motifs and composite modules were found to be significantly enriched in the auxin-responsive promoters from Arabidopsis and rice.
Motifs and composite modules can be analyzed on Watson strands only or include their Crick strand in the calculation ("auto-antisense").
In order to explore if composite modules could also have a 5' to 3' bias, cis-element modules were analysed in both orientations, while allowing the single embedded cis-motifs to be identified on both strands as Watson or Crick words.
In this study, promoters (-1000 nt from TSS) of the auxin inducible genes in comparison to a randomized full genomic promoter dataset were enriched in AuxRE-, bZIP- and MYB-related elements and some of their composite modules in both genomes.
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