This study reveals the evolution of products into designs with smaller part counts, closely matching the modules identified by the conceptual DFA method.
List of coexpression modules identified by MCODE.
The modules identified by ISA are threshold-dependent.
In comparison with traditional clustering methods, the modules identified by ISA are associated with conditions.
The candidate modules identified by Miso 0,1) are exactly the clusters arising in the dendrogram.
The modules identified by the analysis are important because they reflect fundamental structural and functional components of skeletal muscle biology.
Second, the two largest modules identified by network analysis correspond very closely to the three critical signaling pathways identified in the original TCGA pathway analysis.
However, we found that the modules identified by jActiveModules were very large (Figure 3B), typically an order of magnitude larger than those of DEGAS, making them very difficult to interpret and use for derivation of biologically or clinically relevant insights.
We generated random bipartite networks with prescribed modules and used normalized mutual information (NMI) [16] to evaluate the consistency between the prescribed modules and the modules identified by the search method.
All the tissue-related modules were identified using the ISA algorithm proposed by Bergmann et al. [20] which over-performs many traditional clustering approaches in two main aspects: 1) the modules identified by ISA are highly self-consistent; 2) the genes within a module are allowed to be involved in alternative modules [19].
All the other analyses presented below were based on the RMP modules identified by applying Tc = 1.5 and Tg = 3.0 (Actually, the modules identified using other parameters showed similar results regarding the interspecies differences, but these modules were not suitable for the analysis of evolutionary pattern due to their limited number).
