Methods to Reconstruct and Compare Transcriptional Regulatory Networks View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2009-03-10

AUTHORS

M. Madan Babu , Benjamin Lang , L. Aravind

ABSTRACT

The availability of completely sequenced genomes and the wealth of literature on gene regulation have enabled researchers to model the transcriptional regulation system of some organisms in the form of a network. In order to reconstruct such networks in non-model organisms, three principal approaches have been taken. First, one can transfer the interactions between homologous components from a model organism to the organism of interest. Second, microarray experiments can be used to detect patterns in gene expression that stem from regulatory interactions. Finally, knowledge of experimentally characterized transcription factor binding sites can be used to analyze the promoter sequences in a genome in order to identify potential binding sites. In this chapter, we will focus in detail on the first approach and describe methods to reconstruct and analyze the transcriptional regulatory networks of uncharacterized organisms by using a known regulatory network as a template. More... »

PAGES

163-180

References to SciGraph publications

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  • 2004-02. Network biology: understanding the cell's functional organization in NATURE REVIEWS GENETICS
  • 2001-02. Regulatory element detection using correlation with expression in NATURE GENETICS
  • 2005-04. Reverse engineering of regulatory networks in human B cells in NATURE GENETICS
  • 2006-12. CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks in BMC GENOMICS
  • 2002-05. Network motifs in the transcriptional regulation network of Escherichia coli in NATURE GENETICS
  • 2003-11. Computational discovery of gene modules and regulatory networks in NATURE BIOTECHNOLOGY
  • 2003-06. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data in NATURE GENETICS
  • 2004-10. Reconstruction of regulatory and metabolic pathways in metal-reducing δ-proteobacteria in GENOME BIOLOGY
  • 2002-05. Topological and causal structure of the yeast transcriptional regulatory network in NATURE GENETICS
  • 2001-06. Computational analysis of microarray data in NATURE REVIEWS GENETICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/978-1-59745-243-4_8

    DOI

    http://dx.doi.org/10.1007/978-1-59745-243-4_8

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1022850716

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/19381525


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    N-Triples is a line-based linked data format ideal for batch operations.

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    Turtle is a human-readable linked data format.

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    RDF/XML is a standard XML format for linked data.

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