Advanced search
1 file | 1.54 MB Add to list

PheNetic: network-based interpretation of unstructured gene lists in E. coli

(2013) MOLECULAR BIOSYSTEMS. 9(7). p.1594-1603
Author
Organization
Project
Abstract
At the present time, omics experiments are commonly used in wet lab practice to identify leads involved in interesting phenotypes. These omics experiments often result in unstructured gene lists, the interpretation of which in terms of pathways or the mode of action is challenging. To aid in the interpretation of such gene lists, we developed PheNetic, a decision theoretic method that exploits publicly available information, captured in a comprehensive interaction network to obtain a mechanistic view of the listed genes. PheNetic selects from an interaction network the sub-networks highlighted by these gene lists. We applied PheNetic to an Escherichia coli interaction network to reanalyse a previously published KO compendium, assessing gene expression of 27 E. coli knock-out mutants under mild acidic conditions. Being able to unveil previously described mechanisms involved in acid resistance demonstrated both the performance of our method and the added value of our integrated E. coli network.
Keywords
PH REGULATION, SHIGELLA LEXNERI, EXPRESSION, STRESS, CATABOLISM, PROTEIN, REGULATORY PATHWAY INFERENCE, ESCHERICHIA COLI, INTEGRATIVE APPROACH, ACID RESISTANCE

Downloads

  • (...).pdf
    • full text
    • |
    • UGent only
    • |
    • PDF
    • |
    • 1.54 MB

Citation

Please use this url to cite or link to this publication:

MLA
De Maeyer, Dries, Joris Renkens, Lore Cloots, et al. “PheNetic: Network-based Interpretation of Unstructured Gene Lists in E. Coli.” MOLECULAR BIOSYSTEMS 9.7 (2013): 1594–1603. Print.
APA
De Maeyer, D., Renkens, J., Cloots, L., De Raedt, L., & Marchal, K. (2013). PheNetic: network-based interpretation of unstructured gene lists in E. coli. MOLECULAR BIOSYSTEMS, 9(7), 1594–1603.
Chicago author-date
De Maeyer, Dries, Joris Renkens, Lore Cloots, Luc De Raedt, and Kathleen Marchal. 2013. “PheNetic: Network-based Interpretation of Unstructured Gene Lists in E. Coli.” Molecular Biosystems 9 (7): 1594–1603.
Chicago author-date (all authors)
De Maeyer, Dries, Joris Renkens, Lore Cloots, Luc De Raedt, and Kathleen Marchal. 2013. “PheNetic: Network-based Interpretation of Unstructured Gene Lists in E. Coli.” Molecular Biosystems 9 (7): 1594–1603.
Vancouver
1.
De Maeyer D, Renkens J, Cloots L, De Raedt L, Marchal K. PheNetic: network-based interpretation of unstructured gene lists in E. coli. MOLECULAR BIOSYSTEMS. 2013;9(7):1594–603.
IEEE
[1]
D. De Maeyer, J. Renkens, L. Cloots, L. De Raedt, and K. Marchal, “PheNetic: network-based interpretation of unstructured gene lists in E. coli,” MOLECULAR BIOSYSTEMS, vol. 9, no. 7, pp. 1594–1603, 2013.
@article{4180210,
  abstract     = {{At the present time, omics experiments are commonly used in wet lab practice to identify leads involved in interesting phenotypes. These omics experiments often result in unstructured gene lists, the interpretation of which in terms of pathways or the mode of action is challenging. To aid in the interpretation of such gene lists, we developed PheNetic, a decision theoretic method that exploits publicly available information, captured in a comprehensive interaction network to obtain a mechanistic view of the listed genes. PheNetic selects from an interaction network the sub-networks highlighted by these gene lists. We applied PheNetic to an Escherichia coli interaction network to reanalyse a previously published KO compendium, assessing gene expression of 27 E. coli knock-out mutants under mild acidic conditions. Being able to unveil previously described mechanisms involved in acid resistance demonstrated both the performance of our method and the added value of our integrated E. coli network.}},
  author       = {{De Maeyer, Dries and Renkens, Joris and Cloots, Lore and De Raedt, Luc and Marchal, Kathleen}},
  issn         = {{1742-206X}},
  journal      = {{MOLECULAR BIOSYSTEMS}},
  keywords     = {{PH REGULATION,SHIGELLA LEXNERI,EXPRESSION,STRESS,CATABOLISM,PROTEIN,REGULATORY PATHWAY INFERENCE,ESCHERICHIA COLI,INTEGRATIVE APPROACH,ACID RESISTANCE}},
  language     = {{eng}},
  number       = {{7}},
  pages        = {{1594--1603}},
  title        = {{PheNetic: network-based interpretation of unstructured gene lists in E. coli}},
  url          = {{http://dx.doi.org/10.1039/c3mb25551d}},
  volume       = {{9}},
  year         = {{2013}},
}

Altmetric
View in Altmetric
Web of Science
Times cited: