Exome-based analysis for RNA epigenome sequencing data

Jia Meng; Xiaodong Cui; Manjeet K. Rao; Yidong Chen; Yufei Huang

doi:10.1093/bioinformatics/btt171

Exome-based analysis for RNA epigenome sequencing data

Jia Meng^*, Xiaodong Cui, Manjeet K. Rao, Yidong Chen, Yufei Huang

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

145 Citations (Scopus)

Abstract

Motivation: Fragmented RNA immunoprecipitation combined with RNA sequencing enabled the unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this new type of data call for novel computational techniques.Result: Through examining the connections of RNA epigenome sequencing data with two well-studied data types, ChIP-Seq and RNA-Seq, we unveiled the salient characteristics of this new data type. The computational strategies were discussed accordingly, and a novel data processing pipeline was proposed that combines several existing tools with a newly developed exome-based approach 'exomePeak' for detecting, representing and visualizing the post-transcriptional RNA modification sites on the transcriptome.

Original language	English
Pages (from-to)	1565-1567
Number of pages	3
Journal	Bioinformatics
Volume	29
Issue number	12
DOIs	https://doi.org/10.1093/bioinformatics/btt171
Publication status	Published - 15 Jun 2013
Externally published	Yes

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Meng, J., Cui, X., Rao, M. K., Chen, Y., & Huang, Y. (2013). Exome-based analysis for RNA epigenome sequencing data. Bioinformatics, 29(12), 1565-1567. https://doi.org/10.1093/bioinformatics/btt171

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title = "Exome-based analysis for RNA epigenome sequencing data",

abstract = "Motivation: Fragmented RNA immunoprecipitation combined with RNA sequencing enabled the unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this new type of data call for novel computational techniques.Result: Through examining the connections of RNA epigenome sequencing data with two well-studied data types, ChIP-Seq and RNA-Seq, we unveiled the salient characteristics of this new data type. The computational strategies were discussed accordingly, and a novel data processing pipeline was proposed that combines several existing tools with a newly developed exome-based approach 'exomePeak' for detecting, representing and visualizing the post-transcriptional RNA modification sites on the transcriptome.",

author = "Jia Meng and Xiaodong Cui and Rao, {Manjeet K.} and Yidong Chen and Yufei Huang",

note = "Funding Information: Funding: The William and Ella Medical Research Foundation grant to MKR; National Institutes of Health (NIH-NCI P30CA54174) to YC; National Science Foundation (CCF-0546345) to YH; Qatar National Research Fund (09-874-3-235) to YC and YH. We thank computational support provided by the UTSA Computational Systems Biology Core Facility (NIH RCMI grant 5G12RR013646-12).",

year = "2013",

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doi = "10.1093/bioinformatics/btt171",

language = "English",

volume = "29",

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AU - Meng, Jia

AU - Cui, Xiaodong

AU - Rao, Manjeet K.

AU - Chen, Yidong

AU - Huang, Yufei

N1 - Funding Information: Funding: The William and Ella Medical Research Foundation grant to MKR; National Institutes of Health (NIH-NCI P30CA54174) to YC; National Science Foundation (CCF-0546345) to YH; Qatar National Research Fund (09-874-3-235) to YC and YH. We thank computational support provided by the UTSA Computational Systems Biology Core Facility (NIH RCMI grant 5G12RR013646-12).

PY - 2013/6/15

Y1 - 2013/6/15

N2 - Motivation: Fragmented RNA immunoprecipitation combined with RNA sequencing enabled the unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this new type of data call for novel computational techniques.Result: Through examining the connections of RNA epigenome sequencing data with two well-studied data types, ChIP-Seq and RNA-Seq, we unveiled the salient characteristics of this new data type. The computational strategies were discussed accordingly, and a novel data processing pipeline was proposed that combines several existing tools with a newly developed exome-based approach 'exomePeak' for detecting, representing and visualizing the post-transcriptional RNA modification sites on the transcriptome.

AB - Motivation: Fragmented RNA immunoprecipitation combined with RNA sequencing enabled the unbiased study of RNA epigenome at a near single-base resolution; however, unique features of this new type of data call for novel computational techniques.Result: Through examining the connections of RNA epigenome sequencing data with two well-studied data types, ChIP-Seq and RNA-Seq, we unveiled the salient characteristics of this new data type. The computational strategies were discussed accordingly, and a novel data processing pipeline was proposed that combines several existing tools with a newly developed exome-based approach 'exomePeak' for detecting, representing and visualizing the post-transcriptional RNA modification sites on the transcriptome.

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Exome-based analysis for RNA epigenome sequencing data

Abstract

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