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Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles.

Publication ,  Journal Article
Faith, JJ; Hayete, B; Thaden, JT; Mogno, I; Wierzbowski, J; Cottarel, G; Kasif, S; Collins, JJ; Gardner, TS
Published in: PLoS Biol
January 2007

Machine learning approaches offer the potential to systematically identify transcriptional regulatory interactions from a compendium of microarray expression profiles. However, experimental validation of the performance of these methods at the genome scale has remained elusive. Here we assess the global performance of four existing classes of inference algorithms using 445 Escherichia coli Affymetrix arrays and 3,216 known E. coli regulatory interactions from RegulonDB. We also developed and applied the context likelihood of relatedness (CLR) algorithm, a novel extension of the relevance networks class of algorithms. CLR demonstrates an average precision gain of 36% relative to the next-best performing algorithm. At a 60% true positive rate, CLR identifies 1,079 regulatory interactions, of which 338 were in the previously known network and 741 were novel predictions. We tested the predicted interactions for three transcription factors with chromatin immunoprecipitation, confirming 21 novel interactions and verifying our RegulonDB-based performance estimates. CLR also identified a regulatory link providing central metabolic control of iron transport, which we confirmed with real-time quantitative PCR. The compendium of expression data compiled in this study, coupled with RegulonDB, provides a valuable model system for further improvement of network inference algorithms using experimental data.

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Published In

PLoS Biol

DOI

EISSN

1545-7885

Publication Date

January 2007

Volume

5

Issue

1

Start / End Page

e8

Location

United States

Related Subject Headings

  • Transcription, Genetic
  • Reproducibility of Results
  • Operon
  • Oligonucleotide Array Sequence Analysis
  • Iron
  • Gene Regulatory Networks
  • Gene Expression Regulation, Bacterial
  • Gene Expression Profiling
  • Escherichia coli
  • Developmental Biology
 

Citation

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Faith, J. J., Hayete, B., Thaden, J. T., Mogno, I., Wierzbowski, J., Cottarel, G., … Gardner, T. S. (2007). Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol, 5(1), e8. https://doi.org/10.1371/journal.pbio.0050008
Faith, Jeremiah J., Boris Hayete, Joshua T. Thaden, Ilaria Mogno, Jamey Wierzbowski, Guillaume Cottarel, Simon Kasif, James J. Collins, and Timothy S. Gardner. “Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles.PLoS Biol 5, no. 1 (January 2007): e8. https://doi.org/10.1371/journal.pbio.0050008.
Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, et al. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 2007 Jan;5(1):e8.
Faith, Jeremiah J., et al. “Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles.PLoS Biol, vol. 5, no. 1, Jan. 2007, p. e8. Pubmed, doi:10.1371/journal.pbio.0050008.
Faith JJ, Hayete B, Thaden JT, Mogno I, Wierzbowski J, Cottarel G, Kasif S, Collins JJ, Gardner TS. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 2007 Jan;5(1):e8.
Journal cover image

Published In

PLoS Biol

DOI

EISSN

1545-7885

Publication Date

January 2007

Volume

5

Issue

1

Start / End Page

e8

Location

United States

Related Subject Headings

  • Transcription, Genetic
  • Reproducibility of Results
  • Operon
  • Oligonucleotide Array Sequence Analysis
  • Iron
  • Gene Regulatory Networks
  • Gene Expression Regulation, Bacterial
  • Gene Expression Profiling
  • Escherichia coli
  • Developmental Biology