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‘Omics’ - Analysis of high dimensional Data. Achim Tresch Computational Biology. Topics. Hypergeometric test [Khatri and Draghici 2005] Kolmogorov-Smirnov test [Subramanian et al. 2005]. Gene Set Enrichment. Fisher‘s exact test, once more. Fisher‘s exact test, once more. - PowerPoint PPT Presentation
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Achim TreschComputational Biology
‘Omics’
- Analysis of high
dimensional Data
Topics
• Hypergeometric test [Khatri and Draghici 2005]
• Kolmogorov-Smirnov test [Subramanian et al. 2005]
Gene Set Enrichment
Fisher‘s exact test, once more
Fisher‘s exact test, once more
Gene Ontology Example
559
Gene Ontology Example
(immune response) (macromolecule biosynthesis)
Kolmogorov-Smirnov Test
< 10-10
• Move 1/K up when you see a gene from group a
• Move 1/(N-K) down when you see a gene not in group a
Topics
GO scoring: general problem
GO Independence Assumption
light yellow
GO sets
GO Independence Assumption
light yellow
The elim method
The elim method
Top 10 significant nodes (boxes) obtained with
the elim method
The weight method
The weight method
The weight method
(x)
(x)}
The weight method
Top 10 significant nodes (boxes) obtained with
the elim method
Algorithms Summary
Topics
Top scoring GO term
Significant GO terms in
the ALL dataset
Advantages & Disadvantages for ALL
Prostate cancer progression
838210)log( chromhypochromhypo IIIIg
Prostate cancer progression
Prostate cancer progression
Influence of the p-values adjustment
Simulation Study
Introduce noise
Simulation Study
Simulation Study
Quality of GO scoring methods
10% noise level 40% noise level
Summary
Acknowledgements
Adrian AlexaMPI Saarbrücken
