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Intro PPI alignment Algorithms Results Global alignment of protein-protein interaction networks by graph matching methods. Mikhail Zaslavskiy 1 , Francis Bach 2 and Jean-Philippe Vert 1 1 Mines ParisTech / Institut Curie / INSERM 2 INRIA /

  1. Intro PPI alignment Algorithms Results Global alignment of protein-protein interaction networks by graph matching methods. Mikhail Zaslavskiy 1 , Francis Bach 2 and Jean-Philippe Vert 1 1 Mines ParisTech / Institut Curie / INSERM 2 INRIA / Ecole normale superieure de Paris SMPGD 2010. M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  2. Intro PPI alignment Algorithms Results Outline 1 Biological context 2 Protein-protein interaction network alignment 3 Algorithms 4 Experimental results 5 Conclusions M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  3. Intro PPI alignment Algorithms Results Outline 1 Biological context 2 Protein-protein interaction network alignment 3 Algorithms 4 Experimental results 5 Conclusions M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  4. Intro PPI alignment Algorithms Results Proteins M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  5. Intro PPI alignment Algorithms Results Functional orthologs Species 1 Species 2 f 1 : MKQALAAADDDDAQ... y 1 : MDDDDALGLLLLA... f 2 :MGDXLLMMAALLLL... y 2 : MHHAAKLLDDAS... ... ... Objective : Automatic identification of protein functional orthologs M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  6. Intro PPI alignment Algorithms Results Functional orthologs Species 1 Species 2 f 1 : MKQALAAADDDDAQ... y 1 : MDDDDALGLLLLA... f 2 :MGDXLLMMAALLLL... y 2 : MHHAAKLLDDAS... ... ... Objective : Automatic identification of protein functional orthologs M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  7. Intro PPI alignment Algorithms Results Sequence comparison: best-best blast hits Species 1 Species 2 f 1 : MKQDLARIEQFLDALF... y 1 : MSRLPVLLLLQLLVRGA. . . f 2 : MSKLKIAVSDSCPDCF... y 2 : MELAALCRAGLLLALDA. . . ... ...   y 1 y 2 C = 10 50 C ij -BLAST similarity scores f 1   f 2 27 10 Optimal assignment : f 1 → y 2 , f 2 → y 1 Potential difficulties: y is the best hit for f , but f is not the best hit for y ( y 1 , f ) and ( y 2 , f ) produce very close blast scores. Which one to choose ? M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  8. Intro PPI alignment Algorithms Results Sequence comparison: best-best blast hits Species 1 Species 2 f 1 : MKQDLARIEQFLDALF... y 1 : MSRLPVLLLLQLLVRGA. . . f 2 : MSKLKIAVSDSCPDCF... y 2 : MELAALCRAGLLLALDA. . . ... ...   y 1 y 2 C = 10 50 C ij -BLAST similarity scores f 1   f 2 27 10 Optimal assignment : f 1 → y 2 , f 2 → y 1 Potential difficulties: y is the best hit for f , but f is not the best hit for y ( y 1 , f ) and ( y 2 , f ) produce very close blast scores. Which one to choose ? M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  9. Intro PPI alignment Algorithms Results Sequence comparison: best-best blast hits Species 1 Species 2 f 1 : MKQDLARIEQFLDALF... y 1 : MSRLPVLLLLQLLVRGA. . . f 2 : MSKLKIAVSDSCPDCF... y 2 : MELAALCRAGLLLALDA. . . ... ...   y 1 y 2 C = 10 50 C ij -BLAST similarity scores f 1   f 2 27 10 Optimal assignment : f 1 → y 2 , f 2 → y 1 Potential difficulties: y is the best hit for f , but f is not the best hit for y ( y 1 , f ) and ( y 2 , f ) produce very close blast scores. Which one to choose ? M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  10. Intro PPI alignment Algorithms Results Speciation M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  11. Intro PPI alignment Algorithms Results Speciation M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  12. Intro PPI alignment Algorithms Results Speciation & Duplication M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  13. Intro PPI alignment Algorithms Results Speciation & Duplication M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  14. Intro PPI alignment Algorithms Results Ambiguous assignment resolving Increase the quality of similarity score, 3D structures Protein interactions . . . M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  15. Intro PPI alignment Algorithms Results Ambiguous assignment resolving Increase the quality of similarity score, 3D structures Protein interactions . . . M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  16. Intro PPI alignment Algorithms Results Outline 1 Biological context 2 Protein-protein interaction network alignment 3 Algorithms 4 Experimental results 5 Conclusions M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  17. Intro PPI alignment Algorithms Results Protein interaction networks M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  18. Intro PPI alignment Algorithms Results Protein interaction network Fly interaction network M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  19. Intro PPI alignment Algorithms Results Ambiguous assignment resolving M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  20. Intro PPI alignment Algorithms Results Ambiguous assignment resolving M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  21. Intro PPI alignment Algorithms Results Ambiguous assignment resolving M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  22. Intro PPI alignment Algorithms Results Ambiguous assignment resolving M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  23. Intro PPI alignment Algorithms Results Ambiguous assignment resolving M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  24. Intro PPI alignment Algorithms Results Ambiguous assignment resolving ⇒ Maximize :the number of overlapping edges M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  25. Intro PPI alignment Algorithms Results Ambiguous assignment resolving ⇒ Maximize :the number of overlapping edges M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  26. Intro PPI alignment Algorithms Results Two types of global network alignment Constrained Alignment: Only proteins having close sequence structures may be matched to each other InParanoid clusters: Maximize : J = the number of overlapping edges Balanced Alignment: Let S ij = BLAST ( f i , y j ), then the total sequence similarity � S = S ij f i is matched to y j Maximize : (1 − λ ) J + λ S λ controls the trade-off between J and S . M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  27. Intro PPI alignment Algorithms Results Two types of global network alignment Constrained Alignment: Only proteins having close sequence structures may be matched to each other InParanoid clusters: Maximize : J = the number of overlapping edges Balanced Alignment: Let S ij = BLAST ( f i , y j ), then the total sequence similarity � S = S ij f i is matched to y j Maximize : (1 − λ ) J + λ S λ controls the trade-off between J and S . M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  28. Intro PPI alignment Algorithms Results Two types of global network alignment Constrained Alignment: Only proteins having close sequence structures may be matched to each other InParanoid clusters: Maximize : J = the number of overlapping edges Balanced Alignment: Let S ij = BLAST ( f i , y j ), then the total sequence similarity � S = S ij f i is matched to y j Maximize : (1 − λ ) J + λ S λ controls the trade-off between J and S . M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  29. Intro PPI alignment Algorithms Results Two types of global network alignment Constrained Alignment: S. Bandyopadhyay, R. Sharan and T. Ideker, 2006 : MRF model, approximate solution Our contribution: exact solution by the Message Passing Algorithm Balanced Alignment: S. R. Singh, J. Xu and B. Berger, 2008 : IsoRank algorithm Our contribution: Graph Matching Algorithms M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  30. Intro PPI alignment Algorithms Results Two types of global network alignment Constrained Alignment: S. Bandyopadhyay, R. Sharan and T. Ideker, 2006 : MRF model, approximate solution Our contribution: exact solution by the Message Passing Algorithm Balanced Alignment: S. R. Singh, J. Xu and B. Berger, 2008 : IsoRank algorithm Our contribution: Graph Matching Algorithms M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  31. Intro PPI alignment Algorithms Results Outline 1 Biological context 2 Protein-protein interaction network alignment 3 Algorithms 4 Experimental results 5 Conclusions M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  32. Intro PPI alignment Algorithms Results Constrained Alignment: Message Passing MP is based on a forward-backward recursion similar to the Viterbi recursion for hmm. M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  33. Intro PPI alignment Algorithms Results Constrained Alignment: Message Passing Forward step: compute the number of conserved interactions starting from leaves M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

  34. Intro PPI alignment Algorithms Results Constrained Alignment: Message Passing Forward step: compute the number of conserved interactions starting from leaves M. Zaslavskiy, F. Bach, JP. Vert Global alignment of PPI networks

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