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Algorithms for Molecular Biology, 2006 Team 1 Presenter: Ferhat Ay
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Transcript of Algorithms for Molecular Biology, 2006 Team 1 Presenter: Ferhat Ay
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Decomposition of overlapping protein complexes: A graphtheoretical method for analyzing static and dynamic protein associations
Algorithms for Molecular Biology, 2006Team 1Presenter: Ferhat Ay
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Function in PPI networksA functional group is either a
maximal clique or a set of alternative variants of such complexes/cliques.
A functional module is a union ofoverlapping functional groups.
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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 chordal graph has a corresponding clique tree representation.
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Naïve representation VS Tree of Complexes RepresentationWhich protein in which complex
interacts with each other?Dynamics of the interactionsHow to identify functional
groups?A set of maximum cliques
containing a node are connected?Size of overlap
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Complex Overlap Decomposition
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Representing functional groups by Boolean expressions
B
DA C
E(A B C) v (D E) V V V
Cographs : Graphs which can be represented by Boolean expressions
P4
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Edge Addition
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Reduction to Minimum Vertex Cover
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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.
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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.