Large modules of genes related to iron acquisition, anaerobic energy metabolism and protein degradation are the most predominant in the network, suggesting that they are the major iron-responsive biological pathways in S. oneidensis.
This is important because some cellular functions may involve a single direct protein interaction (small scale), whereas others require more and/or indirect interactions, such as protein complexes (medium scale) and interactions between large modules of proteins (large scale).
The contra-flow in out of mesh condition is analyzed and found that the complete contra-flow arises when spray velocity is less than 1% (or higher for large module) of pitch velocity.
The results show that many of these clusters represent expected downstream effects of the TOR pathway, including changes in nitrogen metabolism, actin polymerization, and autophagy, as well as a large module of RNA processing genes.
A widespread effect of aging was increased expression of inflammation and immune response genes, which involved class I MHC genes (e.g., H2-D1, H2-K1), immunoglobulin chain components (e.g., Igk-V1, Igh-6), and a large module of 40 co-expressed genes known to participate in inflammation and immune processes (see Figures 5 and 6; Additional File 10).
The two largest modules of the coexpression network, module A (2848 genes) and module B (2861 genes), grouped genes with strong general responses to the pathogen.
The large modules (numbers of genes per module are given in fig. 4) "black," "cyan" and "blue" were all significantly associated with the two gonad types, "magenta" with testis and brain and "greenyellow" with ovary and brain.
The module containing DNA packaging and structural proteins is the largest module of the Sf101 phage, and is predicted to contain 15 orfs (orf 1 to 15).
jActiveModules generated several large modules, including a module of 981 nodes in BC and a module of 377 nodes in CCA.
The hierarchical nature of the network allows the definition of large modules with more general functions that contain sub-modules with more specific functions, which are distinguished by sets of unique interactions.
Second, the passenger genes of large modules are enriched with the putative targets of their regulators or drivers.
