This finding is consistent with EM studies in which the presence of RNA pol II induces large motions about the hinge regions between the Mediator modules, while the intra-module topology appears unchanged (Asturias et al., 1999; Davis et al., 2002).
(E Studentnt-testst analysis of the intra-module cross-link violation distance.
Recognizable signatures allow for the identification of each module but intra-module similarity is limited [ 2].
Consideration of the 55 intra-module hub genes from critical regulatory modules revealed a number of signaling and cellular processes were influenced, Figure 5 and Figure S3.
We split the cross-link dataset into two subsets composed of inter-module (8% of the total) and intra-module (92% of the total) cross-links.
(D ) Detailed statistics of cross-link satisfaction for the whole dataset (top), intra-module cross links (middle), and inter-module cross-links (bottom).
Most of the 15 modules identified in the co-expression network have a high level of intra-module connectivity (as expected by the definition of a module) and low inter-module connectivity.
Moreover, we found that these bridges were mainly composed of inter-module connections (25/42; 59.52%), despite the fact that most network connections were intra-module (296/337; 87.83%).
On the other hand there is a potential problem of sensitivity, because many functional modules include genes with different degrees of intra-module co-expression, while the methods are many times applied to datasets in which the complete module is assumed to be over- or under-expressed as a whole.
The modular decomposition of the protein enabled us to characterize residues based on their intra-module connectivity, z and inter-module connectivity or participation coefficient, P. Residues that acted as connector hubs between modules, that is, those with high |P/z| values were found to be those that were known to be protected early during the transition state from experimental evidence [27].
