Differential Protein Network Analysis of the Immune Cell Lineage

Figure 1

Workflow of affinity propagation on the PNSM and the differential network analysis. The known activator genes which drive the differentiation of the main immune cell types (see Table 1) were used to query the list of their target genes as computed from the OntoGeNet algorithm on the ImmGen resource. The protein network neighborhood of each of the 7965 genes assigned to an ImmGen network module of was integrated with their target lineage information, computed from an integrated set of validated protein interaction network databases. Then, using the Simpson similarity index, their PNSM was computed. Affinity propagation or “message passaging” was then applied on the PNSM, to capture features of the immune lineage network. The resulting exemplars computed from the affinity propagation allows for differential functions to be captured through the lineage tree.