New Insights into Network Motif Clusters from the Views of Cellular Localizations and Signal Pathways∗

Biological complex networks, such as protein-protein interaction network (PPIN), represent the underlying living mechanisms in cell. Begin with the PPIN, distinct level modular organizations appear, like so-called network motifs, protein complexes and signal pathways. The network motifs defined as spandrels are highly clustered. Here, the motif clusters are divided into two categories, i.e. inner motif clusters (IMC) and outer motif clusters (OMC), based on protein complexes. IMC contains more network motifs inside some protein complex contrasting to OMC. In topological structure, the IMCs are connected more loosely than OMCs and in biology roles the IMCs mainly located in nucleus and serve for the signal pathways closely related to nucleus while OMCs mainly located in cytoplasm and reach for the signal pathways unrelated to nucleus, moreover, in contrast to OMCs, IMCs can reach less cellular localizations. Therefore, from the protein-protein interaction level, subsets of proteins that define functionally meaningful entities can reveal the underlying living mechanisms in cell.