sgnesR: An R package for simulating gene expression data from an underlying real gene network structure considering delay parameters

Shailesh Tripathi, Jason Lloyd-Price, Andre Ribeiro, Olli Yli-Harja, Matthias Dehmer, Frank Emmert-Streib

    Research output: Contribution to journalArticleScientificpeer-review

    7 Citations (Scopus)
    72 Downloads (Pure)

    Abstract

    Background: sgnesR (Stochastic Gene Network Expression Simulator in R) is an R package that provides an interface to simulate gene expression data from a given gene network using the stochastic simulation algorithm (SSA). The package allows various options for delay parameters and can easily included in reactions for promoter delay, RNA delay and Protein delay. A user can tune these parameters to model various types of reactions within a cell. As examples, we present two network models to generate expression profiles. We also demonstrated the inference of networks and the evaluation of association measure of edge and non-edge components from the generated expression profiles. Results: The purpose of sgnesR is to enable an easy to use and a quick implementation for generating realistic gene expression data from biologically relevant networks that can be user selected. Conclusions: sgnesR is freely available for academic use. The R package has been tested for R 3.2.0 under Linux, Windows and Mac OS X.

    Original languageEnglish
    Article number325
    JournalBMC Bioinformatics
    Volume18
    Issue number1
    DOIs
    Publication statusPublished - 4 Jul 2017
    Publication typeA1 Journal article-refereed

    Keywords

    • Gene expression data
    • Gene network
    • Simulation

    Publication forum classification

    • Publication forum level 1

    ASJC Scopus subject areas

    • Structural Biology
    • Biochemistry
    • Molecular Biology
    • Computer Science Applications
    • Applied Mathematics

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