Differential Protein Network Analysis of the Immune Cell Lineage

Figure 3

Integrated protein interaction networks perspective on the gene regulation networks driving immune cell lineages. The immune cell lineage network is depicted as a bipartite network with multiple edges representation. Each edge represents a protein network exemplar. The multiple edges connect the different node types and reflect the regulator activity superimposed on the multiple protein network exemplars activated by immune lineage regulators. Each relationship is a representation of the gene regulation modules from the ImmGen resource connecting with the known regulators of immune cell lineages. Each edge in the network represents a relationship between an immune cell line lineage type (see legend in Figure 3(1)) and one of the known activating factors regulating the differentiation of that lineage (see Table 1 for list of the known activators used). An edge is drawn in the network if there is connection between a regulator gene (triangle node) and a course module (groups of commonly expressed genes) calculated from OntoGenet (circle nodes). The number of lines between a regulator and a module is a measure of how many “protein network exemplars,” as calculated from the affinity propagation (see main text), are associated to the regulatory module (and therefore a possible measure of the diversity of signaling networks activated in driving the lineage of the immune cell type).