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Title: TRIMER: Transcription Regulation Integrated with Metabolic Regulation

Journal Article · · iScience
 [1];  [2]; ORCiD logo [3];  [1];  [4];  [5];  [3]
  1. Texas A & M Univ., College Station, TX (United States)
  2. USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
  3. Texas A & M Univ., College Station, TX (United States); Brookhaven National Lab. (BNL), Upton, NY (United States). Computational Science Initiative
  4. Brookhaven National Lab. (BNL), Upton, NY (United States). Computational Science Initiative
  5. USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Joint BioEnergy Institute and Environmental Genomics and Systems Biology Division
+ Show Author Affiliations

There has been extensive research in predictive modeling of genome-scale metabolic reaction networks. Living systems involve complex stochastic processes arising from interactions among different biomolecules. For more accurate and robust prediction of target metabolic behavior under different conditions, not only metabolic reactions but also the genetic regulatory relationships involving transcription factors (TFs) affecting these metabolic reactions should be modeled. We have developed a modeling and simulation pipeline enabling the analysis of Transcription Regulation Integrated with Metabolic Regulation: TRIMER. TRIMER utilizes a Bayesian network (BN) inferred from transcriptomes to model the transcription factor regulatory network. TRIMER then infers the probabilities of the gene states relevant to the metabolism of interest, and predicts the metabolic fluxes and their changes that result from the deletion of one or more transcription factors at the genome scale. We demonstrate TRIMER’s applicability to both simulated and experimental data and provide performance comparison with other existing approaches.

Research Organization:
Brookhaven National Laboratory (BNL), Upton, NY (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER); National Science Foundation (NSF)
Grant/Contract Number:
SC0012704; CCF-1553281; 0012704; AC02-05CH11231
OSTI ID:
1824873
Alternate ID(s):
OSTI ID: 1839206; OSTI ID: 1896670
Report Number(s):
BNL-222578-2022-JAAM
Journal Information:
iScience, Vol. 24, Issue 11; ISSN 2589-0042
Publisher:
ElsevierCopyright Statement
Country of Publication:
United States
Language:
English

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