ArticleNucleic acids research2015
PheNetic: network-based interpretation of molecular profiling data.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
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- Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes.BMC genomics · 2021Article
- Transcriptomic Insights into the Effect of Melatonin inAntioxidants (Basel, Switzerland) · 2020Article
- MasterPATH: network analysis of functional genomics screening data.BMC genomics · 2020Article
- Redox Systems Biology: Harnessing the Sentinels of the Cysteine Redoxome.Antioxidants & redox signaling · 2020Review
- Image-Based Dynamic Phenotyping Reveals Genetic Determinants of Filamentation-Mediated β-Lactam Tolerance.Frontiers in microbiology · 2020Article
- IAMBEE: a web-service for the identification of adaptive pathways from parallel evolved clonal populations.Nucleic acids research · 2019Article
- Salmonella Typhi, Paratyphi A, Enteritidis and Typhimurium core proteomes reveal differentially expressed proteins linked to the cell surface and pathogenicity.PLoS neglected tropical diseases · 2019Article
- Article
- EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.Nucleic acids research · 2018Article
- Molecular processes underlying synergistic linuron mineralization in a triple-species bacterial consortium biofilm revealed by differential transcriptomics.MicrobiologyOpen · 2018Article
- Network-Based Identification of Adaptive Pathways in Evolved Ethanol-Tolerant Bacterial Populations.Molecular biology and evolution · 2017Article
- Elucidation of the Mode of Action of a New Antibacterial Compound Active against Staphylococcus aureus and Pseudomonas aeruginosa.PloS one · 2016Article
- Adaptation to High Ethanol Reveals Complex Evolutionary Pathways.PLoS genetics · 2015Article
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5 authors.
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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 user-friendly 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 regulatory mechanism 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/.
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