Bioinformatics and Gene Expression Analysis Group

Group Leader

Dr Victoria Perreau

Research Focus

Unlike many bioinformaticians Dr. Perreau comes from a biological research background. Completing both PhD and post doc studies in molecular biology. She has many years of experience at the wet bench investigating RNA expression in many aspects of health and disease in the CNS through the application of micro array analysis. Her research focus in now primarily on computer-based analysis and ‘in silico' research specializing on bioinformatics analysis in the neurosciences with a position in the Centre for Neurosciences. In this position she assists in both experimental design and analysis of micro array experiments including advice on MIAME (minimum information about micro array experiment). Her wet bench experience provides her with a unique insight into the application of micro array technology to the neurosciences and enables her to also offer advice on RNA extraction methods quality control assessment prior to hybridization.

In addition to utilization of many freely distributed software resources, the centre maintains licenses for specialist software analysis tools for analysis of differential expression and pathway analysis.

Dr. Perreau is currently involved collaborative micro array analysis projects with a number of laboratories within the Howard Florey Institute and maintains international collaborations. Additionally she provides bioinformatics services, offering both experimental design and analysis of micro array data services through the National Neurosciences Facility (NNF) Neurogenomics and Neuroproteomics platform.

Honours Project for 2006

Bioinformatics analysis and RT-PCR validation of micro array expression data of neuronal outgrowth

Supervisors

Dr. Victoria Perreau. Phone 8344 1835

Email: vperreau@unimelb.edu.au

A/Prof. Ann Turnley. Phone 8344 3981

Email: turnley@unimelb.edu.au

Laboratory overview

A research focus of the laboratory is the regulation and expression of suppressor of cytokine signaling protein SOCS2, a potent regulator of neuronal differentiation and neurite outgrowth. Information resulting from this project will be integral in the design of a subsequent oligonucleotide micro array experiment to further elucidate the regulation of neurite outgrowth. The Bioinformatics analysis will be performed in conjunction with Dr Perreau at the NNF, while bench work will be performed in the Neural Regeneration Laboratory in the Centre for Neuroscience.

Project overview

This project will provide an introduction to bioinformatics with a strong emphasis on the application of a variety of bioinformatics analysis techniques to specific biological questions through a combination of both ‘in silico' and ‘in vitro' components. These tools will be used to identify and examine factors involved in CNS regeneration after injury.

The number of micro array data sets accessible through data repositories on various websites is rapidly increasing. However there is currently a chronic underutilization of existing experimental data to answer novel research questions. Our interests in CNS regeneration pose many questions regarding SOCS2 regulation and expression, which can be asked of available data. In addition there is growing evidence that there may be a number of interacting and/or overlapping pathways involved in promoting neuronal outgrowth.

The utilization of variety of available micro array expression paradigms, examining neuronal outgrowth under different conditions is an opportunity to identify and segregate gene expression changes in clusters of genes involved in neuronal outgrowth, including SOCS2. A number of published micro array experiments involving neurite outgrowth have been identified and will be utilized. These experimental data will be downloaded and examined using Bioinformatics analysis techniques to identify clusters of genes modulated with neurite outgrowth, focusing on SOCS2 and co-regulated genes. Upstream regulatory sequence analysis will be employed to identify common regulatory motifs within clusters of co-regulated genes. Pathway analysis will also be used to identify activated signaling cascades and examine signaling activation in the different experimental paradigms studied.

The project will culminate in wet bench validation of SOCS2 co regulated target genes identified through the analysis, using SOCS2 over expression cell lines with and without NGF treatment.

The student will be encouraged to identify additional datasets that may contribute to the analysis and explore the application of numerous bioinformatics tools (database searching, micro array expression analysis, transcription factor binding site analysis). An essential component of the project is wet-bench validation of targets identified through the analysis (tissue culture, RNA extraction and purification, Real time PCR).

Selected Publications

Perreau, V. M., Adlard, P.A., Anderson A.J., Cotman C. W. (2005). Exercise induced gene expression changes in the rat spinal cord. In press. Gene Expression.

Perreau, V. M., Aimone, J. B., Leasure, L., Thallmair, M., and the Consortium on Spinal Cord Injury Christopher Reeve Paralysis Foundation (2004). Spatial and temporal gene expression profiling of the contused rat spinal cord. Experimental Neurology Vol. 189 pp204-221.

J, Glaser, R, Gonzalez, V. M. Perreau , C. W. Cotman, H. S. Keirstead. (2004) Neutralization of the chemokine CXCL10 enhances tissue sparing and angiogenesis following spinal cord injury. Journal of Neuroscience Research vol. 77 pp701-708.

Tong, L., Shen, H., Perreau, V. M ., Balazs, R. and Cotman, C. W. (2001). Effects of exercise on gene expression profile in the rat hippocampus. Neurobiology of Disease vol. 8 pp1046-1056.

Contact Us:

Bioinformatics and Gene Expression Analysis Group

Centre for Neuroscience

University of Melbourne Vic 3010

vperreau@unimelb.edu.au