Biological networks are useful approaches to get a view of a biological systems and molecules in their environment at different scales depending on the type of networks. In our work, we use several network representations which include protein-protein interactions networks (PPIN), regulatory networks (RN) and residue interaction networks (RIN). For PPIN and RN nodes represent individual proteins, with the edges either a physical (PPIN) or regulatory (RN) interaction. For RIN the individual residues of a protein (or protein complex) constitute the nodes, with the edges representing a
physical (Van der Waals or Coulomb) interaction. We have developed a tool called RINspector that performs centrality analyses of RIN coupled with flexibility prediction of the corresponding protein chains (more information here).
Two projects are currently running which integrate biological networks :
- Ets-1 : we want to elucidate the role of the Ets-1 oncoprotein in cellular pathways by interaction and regulatory network analyses, mapping public expression data sets onto those networks. These analyses could lead to the identification of novel interaction partners that contribute to an understanding of the cellular signaling that involves Ets-1. Residue interaction networks of predicted complexes between Ets-1 and partners are generated to highlight key residues involved in interactions.
- B4GALNT2 : we want to decipher the regulation of the B4GALNT2 by the creation and analysis of interaction and regulatory networks of regulators of the gene. We want to map expression data onto these networks to help to settle hypotheses that describe B4GALNT2 regulatory systems.