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Algorithms for Molecular Biology, 2006 Team 1 Presenter: Ferhat Ay

Decomposition of overlapping protein complexes: A graph theoretical method for analyzing static and dynamic protein associations. Algorithms for Molecular Biology, 2006 Team 1 Presenter: Ferhat Ay. Function in PPI networks.

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Algorithms for Molecular Biology, 2006 Team 1 Presenter: Ferhat Ay

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  1. Decomposition of overlapping protein complexes: A graphtheoretical method for analyzing static and dynamic protein associations Algorithms for Molecular Biology, 2006 Team 1 Presenter: Ferhat Ay

  2. Function in PPI networks • A functional group is either a maximal clique or a set of alternative variants of such complexes/cliques. • A functional module is a union of overlapping functional groups.

  3. Clique trees can be constructed only for chordal graphs • Chord = an edge connecting two non-consecutive nodes of a cycle • Chordal graph – every cycle of length at least four has a chord. Every chordalgraph has a corresponding clique tree representation.

  4. Naïve representation VS Tree of Complexes Representation • Which protein in which complex interacts with each other? • Dynamics of the interactions • How to identify functional groups? • A set of maximum cliques containing a node are connected? • Size of overlap

  5. Complex Overlap Decomposition

  6. (A B C) v (D E) V V V A C D E B Representing functional groups by Boolean expressions Cographs: Graphs which can be represented by Boolean expressions P4

  7. Edge Addition

  8. Reduction to Minimum Vertex Cover

  9. When it works? • Algorithm is not guaranteed to produce the Tree of Complexes representation. • Conjectured that the algorithm will succeed for chordal graphs and cographs. • Applicable to PPI networks that do not contain long (longer than four node) chordless cycles. • Not appropriate for analyzing large PPI networks with long cycles.

  10. Summary • A new method delineating functional groups and representing their overlaps • Each functional group is represented as a Boolean expression • If functional groups represent dynamically changing protein associations, the method can suggest a possible order of these dynamic changes • For static functional groups it provides compact tree representation of overlaps between such groups • Can be used for predicting protein-protein interactions and putative associations and pathways • Uses chordal graph theory and cograph theory to build new graph-theoretical results.

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