Computational modelling of genome-side transcription assembly networks using a fluidics analogy

Yousry Y. Azmy, Anshuman Gupta, B. Franklin Pugh

Research output: Contribution to journalArticle

Abstract

Understanding how a myriad of transcription regulators work to modulate mRNA output at thousands of genes remains a fundamental challenge in molecular biology. Here we develop a computational tool to aid in assessing the plausibility of gene regulatory models derived from genome-wide expression profiling of cells mutant for transcription regulators. mRNA output is modelled as fluid flow in a pipe lattice, with assembly of the transcription machinery represented by the effect of valves. Transcriptional regulators are represented as external pressure heads that determine flow rate. Modelling mutations in regulatory proteins is achieved by adjusting valves' on/off settings. The topology of the lattice is designed by the experimentalist to resemble the expected interconnection between the modelled agents and their influence on mRNA expression. Users can compare multiple lattice configurations so as to find the one that minimizes the error with experimental data. This computational model provides a means to test the plausibility of transcription regulation models derived from large genomic data sets.

Original languageEnglish (US)
Article numbere3095
JournalPloS one
Volume3
Issue number8
DOIs
StatePublished - Aug 28 2008

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Fluidics
Transcription
transcription (genetics)
Genes
Genome
Messenger RNA
genome
transcription factors
Regulator Genes
Molecular biology
Molecular Biology
regulatory proteins
regulator genes
pipes
topology
molecular biology
Machinery
Pressure
Flow of fluids
Mutation

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

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Computational modelling of genome-side transcription assembly networks using a fluidics analogy. / Azmy, Yousry Y.; Gupta, Anshuman; Pugh, B. Franklin.

In: PloS one, Vol. 3, No. 8, e3095, 28.08.2008.

Research output: Contribution to journalArticle

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