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    Distributed gene expression modelling for exploring variability in epigenetic function

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    Author
    Budden, DM; Crampin, EJ
    Date
    2016-11-05
    Source Title
    BMC Bioinformatics
    Publisher
    BMC
    University of Melbourne Author/s
    Crampin, Edmund; Budden, David Mark
    Affiliation
    School of Mathematics and Statistics
    Metadata
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    Document Type
    Journal Article
    Citations
    Budden, D. M. & Crampin, E. J. (2016). Distributed gene expression modelling for exploring variability in epigenetic function. BMC BIOINFORMATICS, 17 (1), https://doi.org/10.1186/s12859-016-1313-1.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/257064
    DOI
    10.1186/s12859-016-1313-1
    Abstract
    BACKGROUND: Predictive gene expression modelling is an important tool in computational biology due to the volume of high-throughput sequencing data generated by recent consortia. However, the scope of previous studies has been restricted to a small set of cell-lines or experimental conditions due an inability to leverage distributed processing architectures for large, sharded data-sets. RESULTS: We present a distributed implementation of gene expression modelling using the MapReduce paradigm and prove that performance improves as a linear function of available processor cores. We then leverage the computational efficiency of this framework to explore the variability of epigenetic function across fifty histone modification data-sets from variety of cancerous and non-cancerous cell-lines. CONCLUSIONS: We demonstrate that the genome-wide relationships between histone modifications and mRNA transcription are lineage, tissue and karyotype-invariant, and that models trained on matched -omics data from non-cancerous cell-lines are able to predict cancerous expression with equivalent genome-wide fidelity.

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