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Network comparison

Network comparison. Sylvain Brohée. Network comparison. Given two networks Q and R (i.e., protein–protein interaction networks from two different experiments), one would like to compare them in different way. Operations Q inter R Q union R Difference Q not R Difference R not Q

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Network comparison

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  1. Network comparison Sylvain Brohée Sylvain Brohée <sylvain@bigre.ulb.ac.be> Université Libre de Bruxelles, Belgique Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) http://www.bigre.ulb.ac.be/

  2. Network comparison • Given two networks Q and R (i.e., protein–protein interaction networks from two different experiments), one would like to compare them in different way. • Operations • Q inter R • Q union R • Difference Q not R • Difference R not Q • Applications • Comparison of an network obtained from experiment (high-throughput proteomics) to a reference network and assess the quality of the high-throughput method (e.g. Von Mering, 2002). • Union of several networks to get a integrated network that should be more complete • E.g. Unifying protein interaction networks from various sources. • E.g. STRING: integration of data from proteomics, expression, literature, comparative genomics, ... • Intersection between several networks to extract the most relevant relationships, i.e. those supported by multiple evidences.

  3. Principle Query Number of nodes = 7 Number of edges = 9 (Nq)‏ Reference Number of nodes = 8 Number of edges = 12 (Nr)‏ Union Number of nodes = 8 Number of edges = 13 (Nu)‏ Number of edges in common = 8 (Ni)‏ Max number of edges = (8*7)/2 = 28 (Nm)‏

  4. Significance of the intersection Query Number of nodes = 7 Number of edges = 9 (Nq)‏ Reference Number of nodes = 8 Number of edges = 12 (Nr)‏ Jaccard index # Intersection / # Union Nc / Nu = 8 / 13 = 0.61 Union Number of nodes = 8 Number of edges = 13 (Nu)‏ Number of edges in common = 8 (Nc)‏ Max number of edges = (8*7)/2 = 28 (Nm)‏

  5. Significance of the intersection Query Number of nodes = 7 Number of edges = 9 (Nq)‏ Reference Number of nodes = 8 Number of edges = 12 (Nr)‏ Hypergeometric P-value Probability that an intersection of 8 edges or more between both graphs to be reached at random. Union Number of nodes = 8 Number of edges = 13 (Nu)‏ Number of edges in common = 8 (Nc)‏ Max number of edges = (8*7)/2 = 28 (Nm)‏

  6. Study case • Comparison of the two first large scale two hybrid studies dedicated to the yeast interactome. Uetz et al, 2000, Nature Ito et al, 2001, Nature

  7. Dataset description Uetz et al, 2000, Nature Ito et al, 2001, Nature 926 proteins 865 interactions 779 proteins 786 interactions

  8. Uetz et al (2000) vs Ito et al (2001)‏ Number of edges in common : 122 Jaccard : 8% P-value : 2.5e-228 Example Uetzet al (2000)‏ Nodes : 926 Edges : 865 Ito et al (2001)‏ Nodes : 779 Edges : 786 743 122 664

  9. Uetz et al (2000) vs Ito et al (2001)‏ Number of edges in common : 122 Jaccard : 8% P-value : 2.5e-228 Example

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