TY - GEN
T1 - Sketching the distribution of transcriptomic features on RNA transcripts with Travis coordinates
AU - Cui, Xiaodong
AU - Wei, Zhen
AU - Zhang, Lin
AU - Liu, Hui
AU - Sun, Lei
AU - Zhang, Shao Wu
AU - Huang, Yufei
AU - Meng, Jia
N1 - Funding Information:
We thank the support from National Natural Science Foundation of China (61401370, 61473232, 91430111, 61170134 and 61301220) to lM, SWZ and LS; Fundamental Research Funds for the Central Universities (20 14QNB47, 2014QNA84) to LZ and HL; Jiangsu Science and Technology Program (BK20140403) to lM; Xi'an Jiaotong-Liverpool University Research Development Fund (RDF-14-02-01) to JM.
Publisher Copyright:
© 2015 IEEE.
PY - 2015/12/16
Y1 - 2015/12/16
N2 - Biological features, such as, genes, transcription factor binding sites, SNPs, etc., are usually denoted with genome-based coordinates as the genomic features. While genome-based representation is usually very effective, it can be tedious to examine the distribution of RNA-related genomic features on RNA transcripts with existing tools due to the conversion and comparison between genome-based coordinates to RNA-based coordinates. We developed here an open source R package Travis for sketching the transcriptomic view of genomic features so as to facilitate the analysis of RNA-related but genome-based coordinates. Internally, Travis package extracts the coordinates relative to the landmarks of transcripts, with which the distribution of RNA-related genomic features can then be conveniently analyzed. We demonstrated the usage of Travis package in analyzing post-transcriptional RNA modifications (5-MethylCytosine and N6-MethylAdenosine) derived from high-throughput sequencing approaches (MeRIP-Seq and RNA BS-Seq). The Travis R package is now publicly available from GitHub: https://github.com/lzcyzm/Travis.
AB - Biological features, such as, genes, transcription factor binding sites, SNPs, etc., are usually denoted with genome-based coordinates as the genomic features. While genome-based representation is usually very effective, it can be tedious to examine the distribution of RNA-related genomic features on RNA transcripts with existing tools due to the conversion and comparison between genome-based coordinates to RNA-based coordinates. We developed here an open source R package Travis for sketching the transcriptomic view of genomic features so as to facilitate the analysis of RNA-related but genome-based coordinates. Internally, Travis package extracts the coordinates relative to the landmarks of transcripts, with which the distribution of RNA-related genomic features can then be conveniently analyzed. We demonstrated the usage of Travis package in analyzing post-transcriptional RNA modifications (5-MethylCytosine and N6-MethylAdenosine) derived from high-throughput sequencing approaches (MeRIP-Seq and RNA BS-Seq). The Travis R package is now publicly available from GitHub: https://github.com/lzcyzm/Travis.
KW - 5-MethylCytosine (m5C)
KW - BS-Seq
KW - Genomic Features
KW - MeRIP-Seq
KW - N6-MethylAdenosine (m6A)
KW - R package
KW - RNA
KW - visualization
UR - http://www.scopus.com/inward/record.url?scp=84962427488&partnerID=8YFLogxK
U2 - 10.1109/BIBM.2015.7359904
DO - 10.1109/BIBM.2015.7359904
M3 - Conference Proceeding
AN - SCOPUS:84962427488
T3 - Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
SP - 1536
EP - 1542
BT - Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
A2 - Schapranow, lng. Matthieu
A2 - Zhou, Jiayu
A2 - Hu, Xiaohua Tony
A2 - Ma, Bin
A2 - Rajasekaran, Sanguthevar
A2 - Miyano, Satoru
A2 - Yoo, Illhoi
A2 - Pierce, Brian
A2 - Shehu, Amarda
A2 - Gombar, Vijay K.
A2 - Chen, Brian
A2 - Pai, Vinay
A2 - Huan, Jun
PB - Institute of Electrical and Electronics Engineers Inc.
T2 - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015
Y2 - 9 November 2015 through 12 November 2015
ER -