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Exact(5)

Upto 55 motifs are sought (of which up to 31 may be associated with the prior PWMs), and each 500 bp module may contain up to 40 motifs.

Thus, the grey module may contain genes that are associated with TGs but are not part of a WGCNA module.

In contrast to the coherent biclusters generated by most methods, an ENIGMA expression module may contain distinctive subpatterns.

Here again, we observed that a given signalling module may contain canonical proteins from a particular pathway as well as proteins from another pathway.

Furthermore, to rule out the possibility that a single module may contain a very large number of enriched GO terms and therefore dominate the contribution from other modules, we also compute the percentage of modules that have at least one enriched GO term at a given significance level.

Similar(55)

Modules may contain several miRNAs and many mRNAs, and both miRNA and mRNAs can be assigned to 0, 1 or multiple modules, and thus modules may overlap.

However, at this stage multiple modules may contain similar genes as if seed genes have similar expression profiles, similar gene modules will be created around these.

Although the EGF module may not contain as much redundancy as the Grb2 module, two pathways leading to the activation of internalized and external EGF receptors contribute to signal transduction.

As specified by the user, BED files may contain either modules of transcription factor binding sites, or transcription factor binding sites with a branch length score (BLS, [ 37]) above a given threshold.

This provides proof of principle that modules lacking obvious previous functional information may contain very important functionally linked metabolic and disease genes.

In addition, a scaffoldin may contain a carbohydrate-binding module (CBM) that allows the cellulosome to target specific carbohydrate substrates [ 20, 25- 28].

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