Differential Protein Network Analysis of the Immune Cell Lineage

Figure 2

Affinity propagation clustering of the protein interaction association similarity matrix of OntoGeNet target module genes. (a) The PNSM is illustrated for both the entire list of target genes computed from the OntoGeNet algorithm on the ImmGen resources. The degree of red color in the heatmap corresponds with the strength of similarity in the protein network for each gene pair. The exemplars as computed from affinity propagation are illustrated in the annotated color bars and the resulting hierarchical clustering (see Table 1 for list of the protein network exemplars). (b) Exemplifies the effect of application of the affinity propagation workflow applied to protein interaction networks, on hubs only. The hub analysis highlights the possible most influential interaction mechanisms activated by the gene regulatory networks (OntoGenet), which govern the immune cell lineage. (c) A differential functional analysis using the Gene Ontology Biological Process (GO-BP) tree is illustrated for two of the computed exemplars. The trajectory of functional significance of GO-PB terms from the two exemplar’s genes from Figure 2(b) (indicated by the arrows) is illustrated through the GO-BP tree. GO-BP terms significant for the gene list within the exemplars are highlighted in a red color.