Since some functional modules represent general biological processes, in this study we have only focused on five functional modules: immune response, apoptosis mechanism, ion transport, protein secretion, and hemostasis-related process.
Genes in these modules are functionally related to metabolic processes (Modules A and B), transmembrane transport (Module A), immune responses (Module C), and exhibit catalytic or transporter activities (Module A), hydrolase (Module B), endopeptidase (Module C), or other activities (Table 1).
The highest scoring term of biological processes from the Gene Ontology enrichment analysis for the turquoise module is immune response (P-value <0.001), whereas the magenta module does not show any significant functional term enrichment (Fig. 2B).
For example, the muscle co-module was enriched in genes involved in glycolysis, the immune co-module in immune response, the testis co-module in sperm motility, and the liver co-module in catabolic processes (see additional file 1).
The biological functions enriched in this module include immune response, which is consistent with immune dysfunction observed in TS [ 9, 10, 69].
These functional modules represent immune response, apoptosis mechanism, ion transport, protein secretion, hemostasis-related processes, signal transduction, transcription-related processes, embryonic morphogenesis and development, metabolism and catabolism, and other processes (proteins not belonging to the above-mentioned functional modules or without GO annotation, Figure 4).
The model presented in this paper is modular, meaning that specific parts of the model (modules) were developed to describe specific mechanisms, i.e., a module to describe blood flow, another module to describe LDL dynamics and oxidation, another module to describe immune response, and another module to describe statin administration, metabolism, and pharmacological effect.
The IA genes co-expression modules were thus designated as followed: NK cells and innate immunity (blue module), Cytokines and molecular histocompatibility complex (MHC) class I (yellow module), Myeloid cells (turquoise module), Cell signaling and lectin (brown module), Cell activation and apoptosis (green module) and Regulation of immune response (red module).
The identification of the enrichment of the functional module underlying the immune response reinforces the important role the immune system plays in defensive mechanisms against invasive C. albicans in the encounter between C. albicans and zebrafish in the infection process.
While some similarities to both luminal A and B subgroups were observed among luminal M2 tumors, a high module score for immune response was also seen, a feature only associated with the HER2 and basal intrinsic subtypes of FBC.
