ArticleBioinformatics (Oxford, England)2018
Novel approaches for bioinformatic analysis of salivary RNA sequencing data for development.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers, 1 of them a synthesis that pooled it.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Peripheral Blood and Salivary Biomarkers of Blood-Brain Barrier Permeability and Neuronal Damage: Clinical and Applied Concepts.Frontiers in neurology · 2020Pooled it
- Differentially Expressed Salivary miRNAs in Temporomandibular Disorders.Orthodontics & craniofacial research · 2025Article
- Exploring the Therapeutic Potential of Salivary Exosomes in Corneal Epithelial Wound Healing.Investigative ophthalmology & visual science · 2025Article
- Global characterization of extrachromosomal circular DNAs in four body fluids.International journal of legal medicine · 2025Article
- Salivary Proteomics & Gene Expression Analysis: Applications in Orthodontics and Oral Health Care Research-A Pilot Project.Biomarker insights · 2025Article
- RNA transcripts in salivary extracellular vesicle cargo isolated from aged populations.Frontiers in aging · 2025Article
- Spitting in the wind?-The challenges of RNA sequencing for biomarker discovery from saliva.International journal of legal medicine · 2024Article
- Characterization of non-invasive oropharyngeal samples and nucleic acid isolation for molecular diagnostics.Scientific reports · 2024Article
- Salivary Exosomes in Health and Disease: Future Prospects in the Eye.International journal of molecular sciences · 2023Review
- Review
- A comprehensive evaluation of skin aging-related circular RNA expression profiles.Journal of clinical laboratory analysis · 2021Article
- One-Year Update on Salivary Diagnostic of COVID-19.Frontiers in public health · 2021Review
- Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop.Frontiers in genetics · 2021Article
- Microbial extracellular RNAs and their roles in human diseases.Experimental biology and medicine (Maywood, N.J.) · 2020Review
- Clinical validity of saliva and novel technology for cancer detection.Biochimica et biophysica acta. Reviews on cancer · 2019Review
- Role of Saliva and Salivary Diagnostics in the Advancement of Oral Health.Journal of dental research · 2019Article
- Characterization of Human Salivary Extracellular RNA by Next-generation Sequencing.Clinical chemistry · 2018Article
- Bioinformatic analysis of endogenous and exogenous small RNAs on lipoproteins.Journal of extracellular vesicles · 2018Article
Corrections and comments
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Authors and funding
18 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.