Book contents
- Frontmatter
- Dedication
- Contents
- Preface
- List of abbreviations
- 1 Introduction
- I Network Reconstruction
- 2 Network Reconstruction: The Concept
- 3 Network Reconstruction: The Process
- 4 Metabolism in Escherichia coli
- 5 Prokaryotes
- 6 Eukaryotes
- 7 Biochemical Reaction Networks
- 8 Metastructures of Genomes
- II Mathematical Properties of Reconstructed Networks
- III Determining the Phenotypic Potential of Reconstructed Networks
- IV Basic and Applied Uses
- V Conceptual Foundations
- 29 Epilogue
- References
- Index
3 - Network Reconstruction: The Process
from I - Network Reconstruction
Published online by Cambridge University Press: 05 February 2015
- Frontmatter
- Dedication
- Contents
- Preface
- List of abbreviations
- 1 Introduction
- I Network Reconstruction
- 2 Network Reconstruction: The Concept
- 3 Network Reconstruction: The Process
- 4 Metabolism in Escherichia coli
- 5 Prokaryotes
- 6 Eukaryotes
- 7 Biochemical Reaction Networks
- 8 Metastructures of Genomes
- II Mathematical Properties of Reconstructed Networks
- III Determining the Phenotypic Potential of Reconstructed Networks
- IV Basic and Applied Uses
- V Conceptual Foundations
- 29 Epilogue
- References
- Index
Summary
A model that proves very inadequate will be quickly rejected, without contributing much to the genesis and progression of knowledge, while a succession of adjustments to a model that is useful, though not perfect, will lead to an increasingly detailed representation of the phenomenon
– Antoine DanchinIn this chapter we describe the process of network reconstruction in general terms and outline the basic underlying concepts. This process is fundamental to systems biology and culminates in a structured knowledge base, or k-base, that contains comprehensive curated biochemical, genetic, and genomic (BiGG) information on the target organism. A k-base can be updated continually as more is learned about the target organism. It is fair to say that once one has performed such a reconstruction, one knows the target organism in great detail.
Building Knowledge Bases
2D genome annotation A bottom-up network reconstruction is effectively a two-dimensional annotation of a genome (Figure 1.8). It includes a list of components (represented as rows in a table) and the known links between them (represented by columns). If all these links are actual chemical interactions, this table is filled with stoichiometric coefficients. The table basically becomes a connectivity map for the network and it is based on the known chemical components of the network and the chemical interactions (covalent transformations or associations) between the components. The network grows as more and more information about the organism becomes available, or as the scope of the reconstruction grows.
Similarity to the DNA sequence assembly process The process of generating the full DNA sequence of a genome is a familiar one (see top part of Figure 3.1). The irreducible unit of a DNA sequence is a base pair (bp). A read is a number of base pairs sequenced as a group. The read length can vary from 30 to 800 bp. Overlap between reads is used to build contigs. These can be quite large, reaching hundreds of thousands of base pairs. Finally, targeted sequencing is then performed to fill in the gaps between the contigs to obtain the full contiguous genomic sequence.
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- Chapter
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- Systems BiologyConstraint-based Reconstruction and Analysis, pp. 33 - 49Publisher: Cambridge University PressPrint publication year: 2015