Other than where specified, these are my notes from the IB07 Conference, and not expressions of opinion. Any errors are probably just due to my
own misunderstanding. 🙂
Protein-protein interaction networks: fundamental for comprehensive systems biology? PPIs are crucial for cellular processes. Structuring the "hairball": modularity is a major design principle of biological systems. Division of networks in modules, i.e. clusters of proteins that are highly connected etc. The integration of HPI Maps meant that they've included over 160,000 interactions between over 17000 proteins. The PPI Network is assembled via data extraction from literature, giving 35000 interactions between 8500 non-redundant proteins (based on EntrezID).
Identification of modular structures: most communities have less than 15 proteins, in the "mesoscale" range of cluster. Membership of proteins were such that most of the proteins attributed to modules are found only in 1 community. The next step is functional interactomics, which is linking modules to functions, and the interactions within and between modular structures. Characterization and annotation of detected modules were done using GO information and expression data.
Cellular localization of modules: analysis based on 20 informative GO categories. Almost half of proteins are assigned to "nucleus". Of 316 modules of k>3, 170 contained only proteins allocated to one location. Co-expression, co-localization, and common functional annotation: correlation of co-expression and co-localization with a modest correlation of 0.27: 34/51 large modules (k>10) are significantly co-expressed.