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.
Highlights
Genomic, proteomic and high-throughput gene expression data, when integrated, can be used to map the interaction networks between genes and proteins
In our study we focus on the gene module and protein submodule detection using a fast greedy modularity optimization technique [18] that is efficient in the analysis of large networks
We present our findings using a exhaustive list of breast cancer genes, proteins and their protein-protein interaction (PPI) network from the Human Protein Reference Database (HPRD) [29] in combination with the comprehensive and wellestablished microarray datasets from breast cancer patients [30,31]
Summary
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. In the case of breast cancer for example, the interaction network of 6004 proteins is, in different combinations, associated with 5732 biological processes (BP), 1930 molecular functions (MF) and 879 cellular components (CC) as specified in the Gene Ontology Annotation (GOA) [3] database. On this scale it is difficult to interpret the organization principle of such networks that may be composed of thousands of structural subunits. The more highly connected subunits participate in multiple biological activities [4]
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