K-Partite cliques of protein interactions: A novel subgraph topology for functional coherence analysis on PPI networks

Many studies are aimed at identifying dense clusters/subgraphs from protein-protein interaction (PPI) networks for protein function prediction. However, the prediction performance based on the dense clusters is actually worse than a simple guilt-by-association method using neighbor counting ideas. This indicates that the local topological structures and properties of PPI networks are still open to new theoretical investigation and empirical exploration. We introduce a novel topological structure called k-partite cliques of protein interactions-a functionally coherent but not-necessarily dense subgraph topology in PPI networks-to study PPI networks. A k-partite protein clique is a maximal k-partite clique comprising two or more nonoverlapping protein subsets between any two of which full interactions are exhibited. In the detection of PPI's maximal k-partite cliques, we propose to transform PPI networks into induced K-partite graphs where edges exist only between the partites. Then, we present a maximal k-partite clique mining (MaCMik) algorithm to enumerate maximal k-partite cliques from K-partite graphs. Our MaCMik algorithm is then applied to a yeast PPI network. We observed interesting and unusually high functional coherence in k-partite protein cliques-the majority of the proteins in k-partite protein cliques, especially those in the same partites, share the same functions, although k-partite protein cliques are not restricted to be dense compared with dense subgraph patterns or (quasi-)cliques. The idea of k-partite protein cliques provides a novel approach of characterizing PPI networks, and so it will help function prediction for unknown proteins.© 2013 Elsevier Ltd

Asymptotic multipartite version of the Alon-Yuster theorem

In this paper, we prove the asymptotic multipartite version of the Alon-Yuster theorem, which is a generalization of the Hajnal-Szemer\'edi theorem: If $k\geq 3$ is an integer, $H$ is a $k$-colorable graph and $\gamma>0$ is fixed, then, for every sufficiently large $n$, where $|V(H)|$ divides $n$, and for every balanced $k$-partite graph $G$ on $kn$ vertices with each of its corresponding $\binom{k}{2}$ bipartite subgraphs having minimum degree at least $(k-1)n/k+\gamma n$, $G$ has a subgraph consisting of $kn/|V(H)|$ vertex-disjoint copies of $H$. The proof uses the Regularity method together with linear programming.Comment: 22 pages, 1 figur

Graph Saturation in Multipartite Graphs

Let $G$ be a fixed graph and let ${\mathcal F}$ be a family of graphs. A subgraph $J$ of $G$ is ${\mathcal F}$-saturated if no member of ${\mathcal F}$ is a subgraph of $J$, but for any edge $e$ in $E(G)-E(J)$, some element of ${\mathcal F}$ is a subgraph of $J+e$. We let $\text{ex}({\mathcal F},G)$ and $\text{sat}({\mathcal F},G)$ denote the maximum and minimum size of an ${\mathcal F}$-saturated subgraph of $G$, respectively. If no element of ${\mathcal F}$ is a subgraph of $G$, then $\text{sat}({\mathcal F},G) = \text{ex}({\mathcal F}, G) = |E(G)|$. In this paper, for $k\ge 3$ and $n\ge 100$ we determine $\text{sat}(K_3,K_k^n)$, where $K_k^n$ is the complete balanced $k$-partite graph with partite sets of size $n$. We also give several families of constructions of $K_t$-saturated subgraphs of $K_k^n$ for $t\ge 4$. Our results and constructions provide an informative contrast to recent results on the edge-density version of $\text{ex}(K_t,K_k^n)$ from [A. Bondy, J. Shen, S. Thomass\'e, and C. Thomassen, Density conditions for triangles in multipartite graphs, Combinatorica 26 (2006), 121--131] and [F. Pfender, Complete subgraphs in multipartite graphs, Combinatorica 32 (2012), no. 4, 483--495].Comment: 16 pages, 4 figure

Imposing Hierarchy on a Graph

This paper investigates a way of imposing a hierarchy on a graph in order to explore relationships between elements of data. Imposing a hierarchy is equivalent to clustering. First a tree structure is imposed on the initial graph, then a k-partite structure is imposed on each previously obtained cluster. Imposing a tree exposes the hierarchical structure of the graph as well as providing an abstraction of the data. In this study three kinds of merge operations are considered and their composition is shown to yield a tree with a maximal number of vertices in which vertices in the tree are associated with disjoint connected subgraphs. These subgraphs are subsequently transformed into k-partite graphs using similar merge operations. These merges also ensure that the obtained tree is proper with respect to the hierarchy imposed on the data. A detailed example of the techniqueâs application in exposing the structure of protein interaction networks is described. The example focuses on the MAPK cell signalling pathway. The merge operations help expose where signal regulation occurs within the pathway and from other signalling pathways within the cell

An extremal theorem in the hypercube

The hypercube Q_n is the graph whose vertex set is {0,1}^n and where two vertices are adjacent if they differ in exactly one coordinate. For any subgraph H of the cube, let ex(Q_n, H) be the maximum number of edges in a subgraph of Q_n which does not contain a copy of H. We find a wide class of subgraphs H, including all previously known examples, for which ex(Q_n, H) = o(e(Q_n)). In particular, our method gives a unified approach to proving that ex(Q_n, C_{2t}) = o(e(Q_n)) for all t >= 4 other than 5.Comment: 6 page

Triangle-free subgraphs of random graphs

Recently there has been much interest in studying random graph analogues of well known classical results in extremal graph theory. Here we follow this trend and investigate the structure of triangle-free subgraphs of $G(n,p)$ with high minimum degree. We prove that asymptotically almost surely each triangle-free spanning subgraph of $G(n,p)$ with minimum degree at least $\big(\frac{2}{5} + o(1)\big)pn$ is $\mathcal O(p^{-1}n)$-close to bipartite, and each spanning triangle-free subgraph of $G(n,p)$ with minimum degree at least $(\frac{1}{3}+\varepsilon)pn$ is $\mathcal O(p^{-1}n)$-close to $r$-partite for some $r=r(\varepsilon)$. These are random graph analogues of a result by Andr\'asfai, Erd\H{o}s, and S\'os [Discrete Math. 8 (1974), 205-218], and a result by Thomassen [Combinatorica 22 (2002), 591--596]. We also show that our results are best possible up to a constant factor.Comment: 18 page

Transversal designs and induced decompositions of graphs

We prove that for every complete multipartite graph $F$ there exist very dense graphs $G_n$ on $n$ vertices, namely with as many as ${n\choose 2}-cn$ edges for all $n$, for some constant $c=c(F)$, such that $G_n$ can be decomposed into edge-disjoint induced subgraphs isomorphic to~$F$. This result identifies and structurally explains a gap between the growth rates $O(n)$ and $\Omega(n^{3/2})$ on the minimum number of non-edges in graphs admitting an induced $F$-decomposition