A Guide to Integrating Transcriptional Regulatory and Metabolic Networks Using PROM (Probabilistic Regulation of Metabolism)

  • Evangelos Simeonidis
  • Sriram Chandrasekaran
  • Nathan D. Price
Part of the Methods in Molecular Biology book series (MIMB, volume 985)


The integration of transcriptional regulatory and metabolic networks is a crucial step in the process of predicting metabolic behaviors that emerge from either genetic or environmental changes. Here, we present a guide to PROM (probabilistic regulation of metabolism), an automated method for the construction and simulation of integrated metabolic and transcriptional regulatory networks that enables large-scale phenotypic predictions for a wide range of model organisms.

Key words

Systems biology Metabolic networks Transcriptional regulatory networks Constraint-based modeling Probabilistic regulation of metabolism Microarray data 



We acknowledge funding from the Grand Duchy of Luxembourg for ES and NDP, a NIH Howard Temin Pathway to Independence Award in Cancer Research, an NSF CAREER grant, and the Camille Dreyfus Teacher-Scholar Program for NDP, and a Howard Hughes Medical Institute Predoctoral Fellowship for SC.


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Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  • Evangelos Simeonidis
    • 1
    • 2
  • Sriram Chandrasekaran
    • 2
    • 3
  • Nathan D. Price
    • 2
  1. 1.Luxembourg Centre for Systems BiomedicineUniversity of LuxembourgEsch-sur-AlzetteLuxembourg
  2. 2.Institute for Systems BiologySeattleUSA
  3. 3.Center for Biophysics and Computational BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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