TIME WARPING OF EVOLUTIONARY DISTANT TEMPORAL GENE EXPRESSION DATA BASED ON NOISE SUPPRESSION Yury Goltsev and Dmitri Papatsenko *Department of Molecular and Cell biology, University of California, Berkeley, USA * BMC Bioinformatics Oct. 2009 1 V C L a b , D e p t . o f C o m p u t e r S c i e n c e , N T H U , T a i w a n
T IME WARPING OF EVOLUTIONARY DISTANT TEMPORAL GENE EXPRESSION DATA BASED ON NOISE SUPPRESSION Yury Goltsev and Dmitri Papatsenko *Department of Molecular.
Dec 19, 2015
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TIME WARPING OF EVOLUTIONARY DISTANT TEMPORAL GENE EXPRESSION DATA BASED ON NOISE SUPPRESSIONYury Goltsev and Dmitri Papatsenko
*Department of Molecular and Cell biology, University of California, Berkeley, USA
* BMC Bioinformatics Oct. 2009
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OVERVIEW
Introduction Dynamic Time Wraping
Kruskal's algorithm Orthologous Genes
Alignments of cell cycles Simulation data Real data
Conclusion Reference
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INTRODUCTION
Dynamic Time Wraping(DTW)
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INTRODUCTION
Dynamic Time Wraping(DTW)
*http://www.evanlin.com/document/DataMiniing/Discovering similar time series patterns with fuzzy clustering and DTW methonds.ppt
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DYNAMIC TIME WRAPING
Kruskal's algorithm
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INTRODUCTION
Orthologous Genes Homology
Budding yeast Fission yeast
Saccharomyces cerevisiae Schizosaccharomyces pombe
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INTRODUCTION
Cell cycles
* Rustici G, et al., Nat Genet. 2004, 36:809-817
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ALIGNMENTS OF CELL CYCLES
Periodic patterns (A,B: simulation data)
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ALIGNMENTS OF CELL CYCLES
Periodic patterns (real data) A – Euclidean distance matrix B – Alignment path
No alignment
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ALIGNMENTS OF CELL CYCLES
Periodic patterns (real data) A – Pearson distance matrix B – Alignment path
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ALIGNMENTS OF CELL CYCLES
Use Pearson distance rather than Euclidean distance
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ALIGNMENTS OF CELL CYCLES
Remove noise from the data(use Gaussian filter) A – Pearson distance matrix B – Alignment path
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ALIGNMENTS OF CELL CYCLES
matching cell cycle markers to good valleys
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ALIGNMENTS OF CELL CYCLES
matching cell cycle markers to good valleys G1 phase is longer in
S.cerevisiae G2 is longer in S.pombe.
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CONCLUSION
Desynchronization of gene expression in evolution
Microarray data and low-level data processing
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REFERENCE
http://dblab.cs.nccu.edu.tw/presentation/DynamicTimeWarping.ppt
http://www.evanlin.com/document/DataMiniing/Discovering similar time series patterns with fuzzy clustering and DTW methonds.ppt
http://Fmccmb.belozersky.msu.ru/2009/Presentations/20090721MCCMB-Papatsenko.ppt
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