Journal Article

Distributed gene expression modelling for exploring variability in epigenetic function

Crampin, Edmund J., Budden, David M.

2016

Overview

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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V
• Subject: Algorithms / Bioinformatics / Biomedical and Life Sciences / Chromatin Immunoprecipitation - methods / Computational Biology - methods / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Epigenetic inheritance / Epigenomics / Gene expression / Gene Expression Profiling / Gene Expression Regulation, Neoplastic / Genome, Human / High-Throughput Nucleotide Sequencing - methods / Histones - genetics / Histones - metabolism / Humans / Karyotypes / Life Sciences / Microarrays / Neoplasms - genetics / Observations / Research Article / Sequence Analysis, DNA - methods / Transcription, Genetic - genetics / Transcriptome analysis