Gene regulatory and signalling networks exhibit distinct topological distributions of motifs

Understanding why some cellular components are conserved across species, while others evolve rapidly is a key question of modern biology. Here we demonstrate that in S. cerevisiae proteins organized in cohesive patterns of interactions are conserved to a significantly higher degree than those that do not participate in such motifs. We find that the conservation of proteins within distinct topological motifs correlates with the motif's inter-connectedness and function and also...

Analysis of the structure of biological networks often uses statistical tests to establish the over-representation of motifs, which are thought to be important building blocks of such networks, related to their biological functions. However, there is disagreement as to the statistical significance of these motifs, and there are potential problems with standard methods for estimating this significance. Exponential random graph models (ERGMs) are a class of statistical model th...

The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression patterns? We tackle this question in silico by examining the ensemble of all regulatory networks which satisfy the constraint of producing a given sequence of gene expressions. We focus on three cell cycle profiles coming from baker's yeas...

Studying the topology of so-called real networks, that is networks obtained from sociological or biological data for instance, has become a major field of interest in the last decade. One way to deal with it is to consider that networks are built from small functional units called motifs, which can be found by looking for small subgraphs whose numbers of occurrences in the whole network are surprisingly high. In this article, we propose to define motifs through a local overre...

A determinant property of the structure of a biological network is the distribution of local connectivity patterns, i.e., network motifs. In this work, a method for creating directed, unweighted networks while promoting a certain combination of motifs is presented. This motif-based network algorithm starts with an empty graph and randomly connects the nodes by advancing or discouraging the formation of chosen motifs. The in- or out-degree distribution of the generated network...

An important part of the analysis of bio-molecular networks is to detect different functional units. Different functions are reflected in a different evolutionary dynamics, and hence in different statistical characteristics of network parts. In this sense, the {\em global statistics} of a biological network, e.g., its connectivity distribution, provides a background, and {\em local deviations} from this background signal functional units. In the computational analysis of biol...

Gene regulatory networks are powerful abstractions of biological systems. Since the advent of high-throughput measurement technologies in biology in the late 90s, reconstructing the structure of such networks has been a central computational problem in systems biology. While the problem is certainly not solved in its entirety, considerable progress has been made in the last two decades, with mature tools now available. This chapter aims to provide an introduction to the basic...

Studying the topology of so-called {\em real networks}, that is networks obtained from sociological or biological data for instance, has become a major field of interest in the last decade. One way to deal with it is to consider that networks are built from small functional units called {\em motifs}, which can be found by looking for small subgraphs whose numbers of occurrences in the whole network of interest are surprisingly high. In this paper, we propose to define motifs ...

Biological and technological networks contain patterns, termed network motifs, which occur far more often than in randomized networks. Network motifs were suggested to be elementary building blocks that carry out key functions in the network. It is of interest to understand how network motifs combine to form larger structures. To address this, we present a systematic approach to define 'motif generalizations': families of motifs of different sizes that share a common architec...

Recent evidence indicates that the abundance of recurring elementary interaction patterns in complex networks, often called subgraphs or motifs, carry significant information about their function and overall organization. Yet, the underlying reasons for the variable quantity of different subgraph types, their propensity to form clusters, and their relationship with the networks' global organization remain poorly understood. Here we show that a network's large-scale topologica...