Reference: Babu MM, et al. (2009) Methods to reconstruct and compare transcriptional regulatory networks. Methods Mol Biol 541:163-80

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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.

Reference Type
Comparative Study | Journal Article | Research Support, N.I.H., Extramural | Research Support, Non-U.S. Gov't | Review
Authors
Babu MM, Lang B, Aravind L
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Gene Ontology Annotations


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Gene/Complex Qualifier Gene Ontology Term Aspect Annotation Extension Evidence Method Source Assigned On Reference

Phenotype Annotations


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Gene Phenotype Experiment Type Mutant Information Strain Background Chemical Details Reference

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Gene Disease Ontology Term Qualifier Evidence Method Source Assigned On Reference

Regulation Annotations


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Regulator Target Direction Regulation Of Happens During Method Evidence

Post-translational Modifications


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Site Modification Modifier Reference

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Genetic Interactions

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Interactor Interactor Allele Assay Annotation Action Phenotype SGA score P-value Source Reference

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Interactor Interactor Assay Annotation Action Modification Source Reference

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Gene Species Gene ID Strain background Direction Details Source Reference