Journal article

Predicting expression: the complementary power of histone modification and transcription factor binding data

David M Budden, Daniel G Hurley, Joseph Cursons, John F Markham, Melissa J Davis, Edmund J Crampin

Epigenetics and Chromatin | BIOMED CENTRAL LTD | Published : 2014

Abstract

BACKGROUND: Transcription factors (TFs) and histone modifications (HMs) play critical roles in gene expression by regulating mRNA transcription. Modelling frameworks have been developed to integrate high-throughput omics data, with the aim of elucidating the regulatory logic that results from the interactions of DNA, TFs and HMs. These models have yielded an unexpected and poorly understood result: that TFs and HMs are statistically redundant in explaining mRNA transcript abundance at a genome-wide level. RESULTS: We constructed predictive models of gene expression by integrating RNA-sequencing, TF and HM chromatin immunoprecipitation sequencing and DNase I hypersensitivity data for two mamm..

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Grants

Awarded by Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology


Funding Acknowledgements

This work was supported by an Australian Postgraduate Award (DMB); the National Breast Cancer Foundation (MJD); the Australian Federal and Victoria State Governments and the Australian Research Council through the ICT Centre of Excellence program, National ICT Australia (NICTA) (DMB, EJC); and the Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology (project number CE140100036) (EJC). The views expressed herein are those of the authors and are not necessarily those of the National Breast Cancer Foundation, NICTA or the Australian Research Council.