National Cancer Research Institute South of England
Prostate Cancer Collaborative
Core Resources

Bioinformatics

Author
Prof Colin Cooper csc@icr.ac.uk
Institute of Cancer Research

Bioinformatics is carried out through links with Dr Colin Campbell at the University of Bristol. The current focus of our activity has been to develop packages that can help with the analysis of microaray data. Packages have been developed so far are to carry out -

  1. Statistical Outlier Test - this identifies clones whose position deviates significantly from the normal distribution of datapoints seen in the array experiment.
  2. Line straighten programme - when raw microarray data is presented on a scatter plot a systematic deviation of the distribution is often observed due to different dynamic responses of the Cy3 and Cy5 dyes (see Figures 1a and 1b). This package corrects this anomaly.

Figure 1a

Figure 1b

  1. Analysis of CGH data using cDNA microarrays - we have developed a method for looking at low copy number gains and losses by CGH onto cDNA microarrays. A statistical package has been developed to identify chromosomal regions where the CGH ratios deviate significantly from normal and hence represents region of genetic gain or loss.
  2. Non-random distribution of clones in the Human Genome: we have been investigating the distribution of clones within the human genome to determine whether non-random clusters of overexpressed genes can be identified. An analytical package is under development to determine whether a non-random distribution is present.

For further information on these statistical tests contact:-

Dr. Colin Campbell,
Dept. of Engineering Mathematics,
Bristol University, Bristol BS8 1TR,
United Kingdom
http://lara.enm.bris.ac.uk/cig/
Tel +44 (0) 117 928 9858
C.Campbell@bristol.ac.uk


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Aetiology and Genetics

Epidemiological Identification of Families
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Diet and Environment
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Molecular Pathology

Links to Cancer Genome Project
Development of Normal Prostate
Microarray Expression Profiling
Candidate Genes
Novel Telomerase Suppressor Genes
Subtractive Hybridization
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Novel Therapies

New Drugs for Prostate Cancer
Intensity Modulated Radiotherapy
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Academic Urology Unit
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Core Resources

Cancer Gene Cloning Lab
Prostate Tissue arrays
Microarray laboratory
Tissue and blood collections
Bioinformatics

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Tumor micro-environment in early prostate cancer

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Contact us on Email: cbell@icr.ac.uk Tel: 0208 643 8901 Fax: 0208 770 7290 This page last modified: 10/11/03