Two-layer modular analysis of gene and protein networks in breast cancer

Abstract

BackgroundGenomic, proteomic and high-throughput gene expression data, when integrated, can be used to map the interaction networks between genes and proteins. Different approaches have been used to analyze these networks, especially in cancer, where mutations in biologically related genes that encode mutually interacting proteins are believed to be involved. This system of integrated networks as a whole exhibits emergent biological properties that are not obvious at the individual network level. We analyze the system in terms of modules, namely a set of densely interconnected nodes that can be further divided into submodules that are expected to participate in multiple biological activities in coordinated manner.ResultsIn the present work we construct two layers of the breast cancer network: the gene layer, where the correlation network of breast cancer genes is analyzed to identify gene modules, and the protein layer, where each gene module is extended to map out the network of expressed proteins and their interactions in order to identify submodules. Each module and its associated submodules are analyzed to test the robustness of their topological distribution. The constituent biological phenomena are explored through the use of the Gene Ontology. We thus construct a “network of networks”, and demonstrate that both the gene and protein interaction networks are modular in nature. By focusing on the ontological classification, we are able to determine the entire GO profiles that are distributed at different levels of hierarchy. Within each submodule most of the proteins are biologically correlated, and participate in groups of distinct biological activities.ConclusionsThe present approach is an effective method for discovering coherent gene modules and protein submodules. We show that this also provides a means of determining biological pathways (both novel and as well those that have been reported previously) that are related, in the present instance, to breast cancer. Similar strategies are likely to be useful in the analysis of other diseases as well.

The modular biochemical reaction network structure of cellular translation

“…The mass distribution modes trace at least two modularized systems (translation and metabolism, Figures 3A and 4) that, by virtue of their chemical isolation from one another, are each able to independently adapt to conditions that the cell may encounter (58). We use the term 'module' here to denote a subset of the nodes in a network that are densely connected while being sparsely connected with nodes in other modules (58,59). Modules can exhibit hierarchical properties and function as key units of adaptive evolution because organismal fitness depends on their performance (32,(60)(61)(62)(63).…”

NetVA: An R Package for Network Vulnerability and Influence Analysis

“…The development of computational models representing complex biological systems of interest and subsequent analysis has been utilized previously for a thorough exploration and understanding of underlying mechanisms and related properties. [6][7][8][9] The analysis and exploration of these complex networks lead to identifying key molecular players having decisive roles in cellular and functional activities. These key molecules, e.g., genes or proteins, may aid in the development of potential diagnostic and therapeutic targets.…”

Architecture and topologies of gene regulatory networks associated with breast cancer, adjacent normal, and normal tissues

“…The network theory-based approach allows us to investigate the vast amount of high-throughput data in a novel way [12, 13]. Genes and their products work together by interacting with each other to perform various essential cellular functions and processes.…”