Journal article
Transcriptional Dynamics Reveal Critical Roles for Non-coding RNAs in the Immediate-Early Response
S Aitken, S Magi, AMN Alhendi, M Itoh, H Kawaji, T Lassmann, CO Daub, E Arner, P Carninci, ARR Forrest, Y Hayashizaki, LM Khachigian, M Okada-Hatakeyama, CA Semple, A Sandelin, C Wells, DA Hume, KM Summers, K Vitting-Seerup, R Andersson Show all
Plos Computational Biology | PUBLIC LIBRARY SCIENCE | Published : 2015
Abstract
The immediate-early response mediates cell fate in response to a variety of extracellular stimuli and is dysregulated in many cancers. However, the specificity of the response across stimuli and cell types, and the roles of non-coding RNAs are not well understood. Using a large collection of densely-sampled time series expression data we have examined the induction of the immediate-early response in unparalleled detail, across cell types and stimuli. We exploit cap analysis of gene expression (CAGE) time series datasets to directly measure promoter activities over time. Using a novel analysis method for time series data we identify transcripts with expression patterns that closely resemble t..
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Funding Acknowledgements
FANTOM5 was made possible by a Research Grant for RIKEN OSC from MEXT to YH, Grant from MEXT for the RIKEN PMI YH, Grant of the Innovative Cell Biology by Innovative Technology (Cell Innovation Program) from the MEXT to YH and Grant from MEXT to the RIKEN CLST. Medical Research Council (UK). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.