GS5002 Academic Professional Skills and Techniques:
International Journal Club on Gene Expression Profile Analysis
Instructor: Professor Wong Limsoon / 2011/2012 Semester 2 / IVLE

Course Description

The possibility of using gene expression profiling by microarrays for diagnostic and prognostic purposes has generated much excitement and research in the last ten years. Nevertheless, a number of issues persist such as how to rectify batch effects (i.e., non-biological variations) [bolstad-2003], how to handle missing values [troyanskaya-2001] and, most importantly, how to identify genes that are meaningful in explaining the difference in disease phenotypes [zhang-2009, venet-2011].

There are three main groups of approaches, that make use of biological pathways (e.g., enzymatic pathways, gene regulatory pathways, and protein interaction networks), for improving gene selection and for transitioning from the selected genes to the understanding of the sequences of causative molecular events. The first group are the overlap analysis methods [doniger-2003, khatri-2005, zeeberg-2003], which test the significance of the intersection of differentially expressed genes with a biological pathway. The second group are the direct group analysis methods [liu-2007, goeman-2004, pavlidis-2002], which test whether a biological pathway is differentially expressed as a whole. The third group are the network-based analysis methods [sivachenko-2007, sohler-2004, soh-2011], which zoom into a subnetwork of a biological pathway and test whether the subnetwork is differentially expressed. All of these approaches have their basis on the fact that every disease phenotype has some underlying biological causes. Therefore, it is reasonable to analyse the gene expression profiles of disease phenotype with respect to the biological contexts provided by biological pathways and protein interaction networks.

In this "journal club", we will read these and other related papers to gain an appreciation of how biological networks can enhance gene expression profile analysis. Each student will be asked to pick and present one of these (or other relevant papers of his choice). Each student will be graded by all fellow students according to:

Reading List (To be further refined)

Contact: Limsoon Wong / Last updated 30/11/2011.