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WIREs Syst Biol Med
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Network biology: a direct approach to study biological function

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Abstract In this paper we discuss the dualism of gene networks and their role in systems biology. We argue that gene networks (1) can serve as a conceptual framework, forming a fundamental level of a phenomenological description, and (2) are a means to represent and analyze data. The latter point does not only allow a systems analysis but is even amenable for a direct approach to study biological function. Here we focus on the clarity of our main arguments and conceptual meaning of gene networks, rather than the causal inference of gene networks from data. WIREs Syst Biol Med 2011 3 379–391 DOI: 10.1002/wsbm.134 This article is categorized under: Biological Mechanisms > Regulatory Biology

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Schematic genotype–environment interaction that emphasizes the potential influence of the environment on the phenotypic appearance of a population.

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Direct study of a biological function by comparison of modules of gene networks, indicated by the gray background, representing a certain molecular function.

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Influence of different environmental factors on the dynamic state of a cell (interaction pattern among genes) and, hence, on the phenotype.

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Extension of the population genetics perspective. Instead of a direct mapping between genotype–environment to the phenotype an intermediate level representing molecular interactions among genes or gene products in the form of a gene network is included.

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Schematic integration of the metabolic (green), transcriptional regulatory (blue), protein (orange), and signaling network (red). The arrows indicate interactions between and within these networks and their color correspond to the gene network where they originate from. The boundary of the metabolic network corresponds also to the cell membrane. Other spacial arrangements are mere visualizations.

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Distinction between causal interactions and association. The transcription factor RAP1 regulates the expression of the transcription factor HSF1 which regulates the expression of REB1. Because these three genes interact with each other causally, in the way described, we draw a full line between them where the arrow indicated the direction of regulation.65

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Biological Mechanisms > Regulatory Biology

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