When investigating the causes for a complex disease, a standard approach is to find genes which have differential expression patterns depending on whether or not test samples exhibit the disease phenotype. These differentially expressed genes are regarded to encode for proteins which are relevant to the underlying biological process. While important individual proteins may be discovered via this approach, the biological function or pathway which is regulated by these proteins cannot be
understood without the context in which the proteins act to perform said function. My research is targeted toward providing this functional context by identifying biological modules in protein interaction networks (PINs). A biological module is a group of interacting molecules which perform a common function and is regarded to be an important organizational scale in biology [1]. This project builds upon results obtained by Lewis et al. [2] showing that functional communities in yeast PINs can be identified at multiple scales. We aim to identify these functional modules in human PINs and use them as a biological vocabulary for understanding the function of differentially expressed genes. A long term aim for this project is to be able to identify activated pathways in phenotypes which are investigated via gene expression profiles. This represents an important step from identifying genes linked with a disease phenotype, to producing biologically testable hypotheses of pathways that may cause a phenotype. <br><br>
 
[1] Hartwell et al., Nature 402 (6761), 1999<br>
[2] Lewis et al., BMC Sys Biol 4 (1), 2010