Abstract

The architecture and dynamics of molecular networks can provide an understanding of complex biological processes complementary to that obtained from the in-depth study of single genes and proteins. With a completely sequenced and well-annotated genome, a fully characterized cell lineage, and powerful tools available to dissect development, Caenorhabditis elegans, among metazoans, provides an optimal system to bridge cellular and organismal biology with the global properties of macromolecular networks. This chapter considers omic technologies available for C. elegans to describe molecular networks--encompassing transcriptional and phenotypic profiling as well as physical interaction mapping--and discusses how their individual and integrated applications are paving the way for a network-level understanding of C. elegans biology.

Highlights

  • The combined power of global approaches to systematically analyze interactions among genes and their products and the phenotypic consequences of in vivo perturbations promises to drive the development of increasingly sophisticated models of the topology, function, and dynamics of C. elegans molecular networks (Figure 1)

  • The C. elegans genome sequence and its annotation laid the foundation for the development of a variety of functional genomic or “omic” approaches to interrogate molecular networks

  • Because most transcripts are expressed at relatively low levels, random sequencing of clones from complementary DNA (cDNA) libraries makes it extremely hard to capture an entire set of full-length cDNAs (Reboul et al, 2003), and the rate of novel sequences identified has reached diminishing returns due to the relative abundance of encoded transcripts in the library (Das et al, 2001)

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Summary

Introduction

The combined power of global approaches to systematically analyze interactions among genes and their products and the phenotypic consequences of in vivo perturbations promises to drive the development of increasingly sophisticated models of the topology, function, and dynamics of C. elegans molecular networks (Figure 1). The C. elegans genome sequence and its annotation laid the foundation for the development of a variety of functional genomic or “omic” approaches to interrogate molecular networks. This chapter reviews the developments underpinning these technologies, giving particular attention to: i) identifying network components, i.e. the complete lists of non-coding and coding transcripts and open reading frames (ORFs); ii) mapping interconnections between these components; iii) systematic perturbation of networks; iv) spatiotemporal dynamics of network components; and v) global network modeling. We summarize the resources emerging from these efforts, current experimental and computational approaches including the integration of different omic datasets, and developments on the horizon

Network components: transcriptome and ORFeome
Genomic databases
Computational predictions
Transcriptome
ORFeome
Network connections: interactome
Network perturbations: phenome
Systematic phenomics
Network dynamics: from transcriptome to localizome
Dynamic transcriptome analyses
In situ and in vivo analyses
Network modeling: “omic” data integration
Perspectives
Findings
42. Abstract
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