RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE)

Ohmiya, Hiroko, Vitezic, Morana, Frith, Martin C., Itoh, Masayoshi, Carninci, Piero, Forrest, Alistair R. R., Hayashizaki, Yoshihide, Lassmann, Timo, FANTOM Consortium, Beckhouse, Anthony, Wells, Christine, Vijayan, Dipti, Mason, Elizabeth, Wolvetang, Ernst, Hitchens, Kelly, Le Cao, Kim-Anh, Nielsen, Lars, Fearnley, Liam, Kenna, Tony and Blumenthal, Antje (2014) RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE). BMC Genomics, 15 . doi:10.1186/1471-2164-15-269

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Author Ohmiya, Hiroko
Vitezic, Morana
Frith, Martin C.
Itoh, Masayoshi
Carninci, Piero
Forrest, Alistair R. R.
Hayashizaki, Yoshihide
Lassmann, Timo
FANTOM Consortium
Beckhouse, Anthony
Wells, Christine
Vijayan, Dipti
Mason, Elizabeth
Wolvetang, Ernst
Hitchens, Kelly
Le Cao, Kim-Anh
Nielsen, Lars
Fearnley, Liam
Kenna, Tony
Blumenthal, Antje
Title RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE)
Journal name BMC Genomics   Check publisher's open access policy
ISSN 1471-2164
Publication date 2014-04-25
Year available 2014
Sub-type Article (original research)
DOI 10.1186/1471-2164-15-269
Open Access Status DOI
Volume 15
Total pages 15
Place of publication London, United Kingdom
Publisher BioMed
Language eng
Formatted abstract
Background
Next generation sequencing based technologies are being extensively used to study transcriptomes. Among these, cap analysis of gene expression (CAGE) is specialized in detecting the most 5’ ends of RNA molecules. After mapping the sequenced reads back to a reference genome CAGE data highlights the transcriptional start sites (TSSs) and their usage at a single nucleotide resolution.

Results
We propose a pipeline to group the single nucleotide TSS into larger reproducible peaks and compare their usage across biological states. Importantly, our pipeline discovers broad peaks as well as the fine structure of individual transcriptional start sites embedded within them. We assess the performance of our approach on a large CAGE datasets including 156 primary cell types and two cell lines with biological replicas. We demonstrate that genes have complicated structures of transcription initiation events. In particular, we discover that narrow peaks embedded in broader regions of transcriptional activity can be differentially used even if the larger region is not.

Conclusions
By examining the reproducible fine scaled organization of TSS we can detect many differentially regulated peaks undetected by previous approaches.
Keyword CAGE
Peak finding
Reproducibility
Hierarchical stability
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Article number 269.

 
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Citation counts: TR Web of Science Citation Count  Cited 9 times in Thomson Reuters Web of Science Article | Citations
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Created: Thu, 26 Jun 2014, 20:49:37 EST by Cathy Fouhy on behalf of Aust Institute for Bioengineering & Nanotechnology