Format

Send to

Choose Destination
Bioinformatics. 2018 Jan 1;34(1):1-8. doi: 10.1093/bioinformatics/btx504.

Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.

Author information

1
Center for Oral/Head & Neck Oncology Research, School of Dentistry, Division of Oral Biology & Medicine University of California at Los Angeles, Los Angeles, CA 90095, USA.
2
Department of Molecular Biophysics and Biochemistry, Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.
3
The Department of Computer Science, Yale University, New Haven, CT 06520.
4
Department of Integrative Biology and Physiology, University of California at Los Angeles, Los Angeles, CA 90095-1570, USA.
5
Department of Oral Medicine, School of Dentistry, Pusan National University, Beomeo-ri, Mulgeum-eup, Yangsan-si, Gyeongsangnam-do 626-770, Korea.
6
Department of Biostatistics, University of California at Los Angeles, Los Angeles, CA 90024, USA.
7
Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul, Korea.
8
Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Gangnam-gu, Seoul, Korea.
9
Department of Pathology & Laboratory Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.
10
Department of Molecular Biophysics and Biochemistry,Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

Abstract

Motivation:

Analysis of RNA sequencing (RNA-Seq) data in human saliva is challenging. Lack of standardization and unification of the bioinformatic procedures undermines saliva's diagnostic potential. Thus, it motivated us to perform this study.

Results:

We applied principal pipelines for bioinformatic analysis of small RNA-Seq data of saliva of 98 healthy Korean volunteers including either direct or indirect mapping of the reads to the human genome using Bowtie1. Analysis of alignments to exogenous genomes by another pipeline revealed that almost all of the reads map to bacterial genomes. Thus, salivary exRNA has fundamental properties that warrant the design of unique additional steps while performing the bioinformatic analysis. Our pipelines can serve as potential guidelines for processing of RNA-Seq data of human saliva.

Availability and implementation:

Processing and analysis results of the experimental data generated by the exceRpt (v4.6.3) small RNA-seq pipeline (github.gersteinlab.org/exceRpt) are available from exRNA atlas (exrna-atlas.org). Alignment to exogenous genomes and their quantification results were used in this paper for the analyses of small RNAs of exogenous origin.

Contact:

dtww@ucla.edu.

PMID:
28961734
PMCID:
PMC5859991
DOI:
10.1093/bioinformatics/btx504
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center