Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features

Year: 2016

Type: article

Abstract: Biological features, such as genes and transcription factor binding sites, are often denoted with genome-based coordinates as the genomic features. While genome-based representation is usually very effective in correlating various biological features, it can be tedious to examine the relationship between RNA-related genomic features and the landmarks of RNA transcripts with existing tools due to the difficulty in the conversion between genome-based coordinates and RNA-based coordinates. We developed here an open source Guitar R/Bioconductor package for sketching the transcriptomic view of RNA-related biological features represented by genome based coordinates. Internally, Guitar package extracts the standardized RNA coordinates with respect to the landmarks of RNA transcripts, with which hundreds of millions of RNA-related genomic features can then be efficiently analyzed within minutes. We demonstrated the usage of Guitar package in analyzing posttranscriptional RNA modifications (5-methylcytosine and N6-methyladenosine) derived from high-throughput sequencing approaches (MeRIP-Seq and RNA BS-Seq) and show that RNA 5-methylcytosine (m(5)C) is enriched in 5'UTR. The newly developed Guitar R/Bioconductor package achieves stable performance on the data tested and revealed novel biological insights. It will effectively facilitate the analysis of RNA methylation data and other RNA-related biological features in the future.

Source: BioMed Research International

DOI: 10.1155/2016/8367534

Authors: Xiaodong Cui, Zhen Wei, Lin Zhang, Hui Liu, Lei Sun, Shao-Wu Zhang, Yufei Huang, Jia Meng

Institutions: The University of Texas at San Antonio, University of Liverpool, Xi’an Jiaotong-Liverpool University, China University of Mining and Technology, Yangzhou University, Northwestern Polytechnical University

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $2,680

Funders: University of Texas at San Antonio, National Natural Science Foundation of China, National Institutes of Health, Fundamental Research Funds for the Central Universities, National Cancer Institute, National Institute of General Medical Sciences, National Institute on Minority Health and Health Disparities

OpenAlex ID: W2345013090