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COMPUTATIONAL ANALYSIS
OF MICROARRAY DATA |
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ABSTRACT |
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Urothelium is a specialised
transitional epithelium, which lines the urinary tract
and gives rise to the most common from of bladder cancer,
transitional cell carcinoma (TCC). It has been suggested
that in order to maintain the urinary barrier and protect
underlying cells, the urothelium will respond to genotoxic
damage through DNA repair and cell survival, rather than
cell death and apoptosis and this will be reflected in
characteristic changes in gene expression. Urothelial
cells were treated with various genotoxic agents, RNA
was extracted from cell monocultures and subsequent microarray
experiments were performed. The produced gene expression
dataset was analysed with PCA and Hierarchical/K-means
clustering to characterise the response of urothelial
cells to genotoxic agents in terms of both cell behaviour
and gene expression changes. |
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For a detailed description of
the analysis and results, download this poster
(PDF - 398kb). |
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Principal component analysis
was performed to reveal any present classification patterns
within the expression dataset investigated. A unimodal
distribution of expression (as illustrated) in the most
informative two dimensions suggested that the genes do
not fall into well-defined clusters. |
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REFERENCES:
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Eisen M.B, Spellman
P.T, Brown P.O, Botstein D, (1998). "Cluster analysis
and diplay of genome wide expression patterns", Proceedings
of Natural Academy of Science USA, 95:14863-68 |
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Quackenbush J, (2001).
"Computational analysis of microarray data",Nature
Genetics Reviews, 2(6):418-427 |
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Thyjaer T, Workman
C, Kruhoffer M, Demtroder K, Wolf H, Andersen L.D, Frederiksen
C.M, Knudsen S, Orntoft T.F, (2001). "Identification
of Gene Expression Patterns in Superficial and Invasive
Human Bladder Cancer", Cancer Research, 61:2492-299 |
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| PREVIOUS PROJECTS: |
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| SNP
Viewer |
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| Kinesins
Structural Bioinformatics |
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| Microarray
Data Analysis |
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| Methylation
Studies in Cancer |
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