Talk by: Dr. Zoran Obradovic, Prof. & Director of IST Center, Temple University

Title: Characterization of Gene Functional Expression Profiles

Abstract:  

Our objective was to provide functional characterization of gene expression related to Intraerythrocytic Developmental Cycle (IDC) of Plasmodium Falciparum. We explored a hypothesis that genes with same or similar function are likely to have similar expression profiles. Analysis of 1,051 Gene Ontology (GO) terms represented by at least two genes in Plasmodium Falciparum microarray data set revealed that gene expression profiles in 550 of them are significantly (P<0.05) correlated. We represented each of the 550 significant GO terms with the functional expression profile defined as average expression profile of all genes annotated with a given GO term. 

Using K-means clustering, we clustered 199 profiles corresponding to GO molecular functions into 4 groups. This was repeated on 228 profiles corresponding to GO biological process. We quantified the clustering quality by introducing a measure of GO term similarity defined as the minimal distance between two GO terms in GO direct acyclic graph. The results based on this measure showed that the obtained clusterings are biologically relevant which supported our hypothesis that genes with similar functions have similar expressions. This indicated that functional expression profiles can provide a valuable tool for analysis and interpretation of microarray data. 

This work is result of joint research with Hongbo Xie, Slobodan Vucetic, Hao Sun, and Pooja Hedge. It will appear at the fifth international conference for the Critical Assessment of Microarray Data Analysis (CAMDA 2004).