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T IME WARPING OF EVOLUTIONARY DISTANT TEMPORAL GENE EXPRESSION DATA BASED ON NOISE SUPPRESSION Yury Goltsev and Dmitri Papatsenko *Department of Molecular.

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Presentation on theme: "T IME WARPING OF EVOLUTIONARY DISTANT TEMPORAL GENE EXPRESSION DATA BASED ON NOISE SUPPRESSION Yury Goltsev and Dmitri Papatsenko *Department of Molecular."— Presentation transcript:

1 T IME 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 VC Lab, Dept. of Computer Science, NTHU, Taiwan

2 O VERVIEW Introduction Dynamic Time Wraping Kruskal's algorithm Orthologous Genes Alignments of cell cycles Simulation data Real data Conclusion Reference 2 VC Lab, Dept. of Computer Science, NTHU, Taiwan

3 I NTRODUCTION Dynamic Time Wraping(DTW) 3 VC Lab, Dept. of Computer Science, NTHU, Taiwan *http://dblab.cs.nccu.edu.tw/presentation/DynamicTimeWarping.ppt

4 I NTRODUCTION Dynamic Time Wraping(DTW) 4 VC Lab, Dept. of Computer Science, NTHU, Taiwan *http://www.evanlin.com/document/DataMiniing/Discovering similar time series patterns with fuzzy clustering and DTW methonds.ppt

5 D YNAMIC T IME W RAPING Kruskal's algorithm 5 VC Lab, Dept. of Computer Science, NTHU, Taiwan *http://Fmccmb.belozersky.msu.ru/2009/Presentations/20090721MCCMB-Papatsenko.ppt

6 I NTRODUCTION Orthologous Genes Homology Budding yeast Fission yeast Saccharomyces cerevisiae Schizosaccharomyces pombe 6 VC Lab, Dept. of Computer Science, NTHU, Taiwan

7 I NTRODUCTION Cell cycles 7 VC Lab, Dept. of Computer Science, NTHU, Taiwan * Rustici G, et al., Nat Genet. 2004, 36:809-817

8 A LIGNMENTS OF CELL CYCLES Periodic patterns (A,B: simulation data) 8 VC Lab, Dept. of Computer Science, NTHU, Taiwan

9 A LIGNMENTS OF CELL CYCLES Periodic patterns (real data) A – Euclidean distance matrix B – Alignment path No alignment 9 VC Lab, Dept. of Computer Science, NTHU, Taiwan

10 A LIGNMENTS OF CELL CYCLES Periodic patterns (real data) A – Pearson distance matrix B – Alignment path 10 VC Lab, Dept. of Computer Science, NTHU, Taiwan

11 A LIGNMENTS OF CELL CYCLES Use Pearson distance rather than Euclidean distance 11 VC Lab, Dept. of Computer Science, NTHU, Taiwan

12 A LIGNMENTS OF CELL CYCLES Remove noise from the data(use Gaussian filter ) A – Pearson distance matrix B – Alignment path 12 VC Lab, Dept. of Computer Science, NTHU, Taiwan

13 A LIGNMENTS OF CELL CYCLES matching cell cycle markers to good valleys 13 VC Lab, Dept. of Computer Science, NTHU, Taiwan

14 A LIGNMENTS OF CELL CYCLES matching cell cycle markers to good valleys G1 phase is longer in S.cerevisiae G2 is longer in S.pombe. 14 VC Lab, Dept. of Computer Science, NTHU, Taiwan

15 C ONCLUSION Desynchronization of gene expression in evolution Microarray data and low-level data processing 15 VC Lab, Dept. of Computer Science, NTHU, Taiwan

16 R EFERENCE http://dblab.cs.nccu.edu.tw/presentation/Dynamic TimeWarping.ppt http://www.evanlin.com/document/DataMiniing/D iscovering similar time series patterns with fuzzy clustering and DTW methonds.ppt http://Fmccmb.belozersky.msu.ru/2009/Presentat ions/20090721MCCMB-Papatsenko.ppt 16 VC Lab, Dept. of Computer Science, NTHU, Taiwan

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