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Protocols

PROM specifications

Information


Unique identifier OMICS_28798
Name PROM
Alternative name Probabilistic Regulation of Metabolism
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Nathan Price

Publications for Probabilistic Regulation of Metabolism

PROM citations

 (11)
library_books

Combining inferred regulatory and reconstructed metabolic networks enhances phenotype prediction in yeast

2017
PLoS Comput Biol
PMCID: 5453602
PMID: 28520713
DOI: 10.1371/journal.pcbi.1005489

[…] We expanded the yeast gene regulatory network derived using EGRIN and presented in [], in order to integrate it with PROM by focusing on predicting regulation for individual genes rather than for gene clusters as had been done previously. The yeast EGRIN was constructed using two computational tools (cMonkey and Inf […]

library_books

Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis

2016
Nat Microbiol
PMCID: 5010021
PMID: 27573104
DOI: 10.1038/nmicrobiol.2016.78

[…] The approach used in this study includes both computational and biological methods. Algorithms developed for the EGRIN model and the PROM model were implemented in the R programming language and MATLAB, respectively. Plots were generated using R, regulatory network diagrams generated using Cytoscape, and images prepared using Adobe […]

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Assessment of FBA Based Gene Essentiality Analysis in Cancer with a Fast Context Specific Network Reconstruction Method

2016
PLoS One
PMCID: 4856428
PMID: 27145226
DOI: 10.1371/journal.pone.0154583
call_split See protocol

[…] conflicts between expressed and non-expressed genes and reactions due to post-transcriptional regulatory events [,]. MIRAGE extends upon MBA accounting, among other things, for biomass production []. PROM [] and E-Flux [] belong to a different family of methods, where maximum allowable fluxes are adjusted using gene expression data. In particular, PROM integrates metabolism with regulatory network […]

library_books

Integration of Metabolic Modeling with Gene Co expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis

2016
Sci Rep
PMCID: 4802306
PMID: 27000948
DOI: 10.1038/srep23440

[…] These approaches include Gene Inactivity Moderated by Metabolism and Expression (GIMME), integrative metabolic analysis tool (iMAT), Metabolic Adjustment by Differential Expression (MADE), E-flux and Probabilistic Regulation of Metabolism (PROM). The GIMME and iMAT use gene expression data to check functionality of reactions in metabolic network using expression level of genes associated with reac […]

library_books

Shikimic Acid Production in Escherichia coli: From Classical Metabolic Engineering Strategies to Omics Applied to Improve Its Production

2015
Front Bioeng Biotechnol
PMCID: 4585142
PMID: 26442259
DOI: 10.3389/fbioe.2015.00145

[…] anscription constraints, as verified by experimental measurements of flux (Åkesson et al., ).Many methods have been developed to introduce transcriptomic regulation into modeling predictions, such as probabilistic regulation of metabolism (PROM), which calculates the probability that a metabolic target gene will be expressed relative to the activity of its regulating transcription factor, metaboli […]

library_books

Metabolic modeling predicts metabolite changes in Mycobacterium tuberculosis

2015
BMC Syst Biol
PMCID: 4574064
PMID: 26377923
DOI: 10.1186/s12918-015-0206-7

[…] ndium of 437 microarray experiments corresponding to 75 different drugs and culture conditions [], we correctly predicted 6 of 7 known inhibitors within this data set []. A more recent method, called Probabilistic Regulation of Metabolism (PROM) [], translates expression data into soft constraints on model reaction rates. PROM generates a flux distribution that is consistent with a set of gene exp […]

Citations

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PROM institution(s)
Institute for Systems Biology, Seattle, WA, USA
PROM funding source(s)
Supported by the Grand Duchy of Luxembourg, a NIH Howard Temin Pathway to Independence Award in Cancer Research, an NSF CAREER grant, and the Camille Dreyfus Teacher-Scholar Program, and a Howard Hughes Medical Institute Predoctoral Fellowship.

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