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PheNetic : network-based interpretation of molecular profiling data

Dries De Maeyer, Bram Weytjens, Joris Renkens, Luc De Raedt and Kathleen Marchal (UGent)
(2015) NUCLEIC ACIDS RESEARCH. 43(W1). p.W244-W250
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Abstract
Molecular profiling experiments have become standard in current wet-lab practices. Classically, enrichment analysis has been used to identify biological functions related to these experimental results. Combining molecular profiling results with the wealth of currently available interactomics data, however, offers the opportunity to identify the molecular mechanism behind an observed molecular phenotype. In this paper, we therefore introduce 'PheNetic', a userfriendly web server for inferring a sub-network based on probabilistic logical querying. PheNetic extracts from an interactome, the sub-network that best explains genes prioritized through a molecular profiling experiment. Depending on its run mode, PheNetic searches either for a regulatorymechanism that gave explains to the observed molecular phenotype or for the pathways (in) activated in the molecular phenotype. The web server provides access to a large number of interactomes, making sub-network inference readily applicable to a wide variety of organisms. The inferred sub-networks can be interactively visualized in the browser. PheNetic's method and use are illustrated using an example analysis of differential expression results of ampicillin treated Escherichia coli cells. The PheNetic web service is available at http://bioinformatics.intec.ugent.be/phenetic/.
Keywords
BIOLOGY, IBCN, MODELS, BACTERIA, PATHWAYS

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MLA
De Maeyer, Dries, et al. “PheNetic : Network-Based Interpretation of Molecular Profiling Data.” NUCLEIC ACIDS RESEARCH, vol. 43, no. W1, 2015, pp. W244–50, doi:10.1093/nar/gkv347.
APA
De Maeyer, D., Weytjens, B., Renkens, J., De Raedt, L., & Marchal, K. (2015). PheNetic : network-based interpretation of molecular profiling data. NUCLEIC ACIDS RESEARCH, 43(W1), W244–W250. https://doi.org/10.1093/nar/gkv347
Chicago author-date
De Maeyer, Dries, Bram Weytjens, Joris Renkens, Luc De Raedt, and Kathleen Marchal. 2015. “PheNetic : Network-Based Interpretation of Molecular Profiling Data.” NUCLEIC ACIDS RESEARCH 43 (W1): W244–50. https://doi.org/10.1093/nar/gkv347.
Chicago author-date (all authors)
De Maeyer, Dries, Bram Weytjens, Joris Renkens, Luc De Raedt, and Kathleen Marchal. 2015. “PheNetic : Network-Based Interpretation of Molecular Profiling Data.” NUCLEIC ACIDS RESEARCH 43 (W1): W244–W250. doi:10.1093/nar/gkv347.
Vancouver
1.
De Maeyer D, Weytjens B, Renkens J, De Raedt L, Marchal K. PheNetic : network-based interpretation of molecular profiling data. NUCLEIC ACIDS RESEARCH. 2015;43(W1):W244–50.
IEEE
[1]
D. De Maeyer, B. Weytjens, J. Renkens, L. De Raedt, and K. Marchal, “PheNetic : network-based interpretation of molecular profiling data,” NUCLEIC ACIDS RESEARCH, vol. 43, no. W1, pp. W244–W250, 2015.
@article{7026955,
  abstract     = {{Molecular profiling experiments have become standard in current wet-lab practices. Classically, enrichment analysis has been used to identify biological functions related to these experimental results. Combining molecular profiling results with the wealth of currently available interactomics data, however, offers the opportunity to identify the molecular mechanism behind an observed molecular phenotype. In this paper, we therefore introduce 'PheNetic', a userfriendly web server for inferring a sub-network based on probabilistic logical querying. PheNetic extracts from an interactome, the sub-network that best explains genes prioritized through a molecular profiling experiment. Depending on its run mode, PheNetic searches either for a regulatorymechanism that gave explains to the observed molecular phenotype or for the pathways (in) activated in the molecular phenotype. The web server provides access to a large number of interactomes, making sub-network inference readily applicable to a wide variety of organisms. The inferred sub-networks can be interactively visualized in the browser. PheNetic's method and use are illustrated using an example analysis of differential expression results of ampicillin treated Escherichia coli cells. The PheNetic web service is available at http://bioinformatics.intec.ugent.be/phenetic/.}},
  author       = {{De Maeyer, Dries and Weytjens, Bram and Renkens, Joris and De Raedt, Luc and Marchal, Kathleen}},
  issn         = {{0305-1048}},
  journal      = {{NUCLEIC ACIDS RESEARCH}},
  keywords     = {{BIOLOGY,IBCN,MODELS,BACTERIA,PATHWAYS}},
  language     = {{eng}},
  number       = {{W1}},
  pages        = {{W244--W250}},
  title        = {{PheNetic : network-based interpretation of molecular profiling data}},
  url          = {{http://doi.org/10.1093/nar/gkv347}},
  volume       = {{43}},
  year         = {{2015}},
}
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