mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing

Wu, Jinyu; Liu, Qi; Wang, Xin; Zheng, Jiayong; Wang, Tao; You, Mingcong; Sun, Zhong Sheng; Shi, Qinghua

doi:10.4161/rna.25193

Cited by 87 publications

(52 citation statements)

References 36 publications

(28 reference statements)

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“…Among the most commonly used tools, miRDeep is applied not only to quantify miRNAs but also to predict potentially novel markers [122,123]. Similar functionality is offered by the UEA workbench [124], the sRNAtoolbox [125], miRExpress [126] or miRTools [127]. Another program tailored for the quantification of miRNAs from NGS data is miRNAKey [128].…”

Section: Post-analytical Aspects: Data Analysis and Results Reportingmentioning

confidence: 99%

miRNA assays in the clinical laboratory: workflow, detection technologies and automation aspects

Kappel

Keller

2017

Clinical Chemistry and Laboratory Medicine (CCLM)

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microRNAs (miRNAs) are short non-coding RNA molecules that regulate gene expression in eukaryotes. Their differential abundance is indicative or even causative for a variety of pathological processes including cancer or cardiovascular disorders. Due to their important biological function, miRNAs represent a promising class of novel biomarkers that may be used to diagnose life-threatening diseases, and to monitor disease progression. Further, they may guide treatment selection or dosage of drugs. miRNAs from blood or derived fractions are particularly interesting candidates for routine laboratory applications, as they can be measured in most clinical laboratories already today. This assures a good accessibility of respective tests. Albeit their great potential, miRNA-based diagnostic tests have not made their way yet into the clinical routine, and hence no standardized workflows have been established to measure miRNAs for patients' benefit. In this review we summarize the detection technologies and workflow options that exist to measure miRNAs, and we describe the advantages and disadvantages of each of these options. Moreover, we also provide a perspective on data analysis aspects that are vital for translation of raw data into actionable diagnostic test results.

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Section: Post-analytical Aspects: Data Analysis and Results Reportingmentioning

confidence: 99%

miRNA assays in the clinical laboratory: workflow, detection technologies and automation aspects

Kappel

Keller

2017

Clinical Chemistry and Laboratory Medicine (CCLM)

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“…Web Server MirTools [24,25] was used to systematically analyze the small RNA sequencing datasets on a large scale.…”

Section: Methodsmentioning

confidence: 99%

Upregulation of Circulating miR-195-3p in Heart Failure

Ji²,

Wang³

et al. 2017

Cardiology

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Objectives: Many circulating microRNAs (miRs) have been shown to have potential biomarker effects in cardiovascular disease. We studied the dysregulation of circulating miR-195-3p in patients with heart failure (HF) to elucidate its value as a potential biomarker for HF. Methods: Eight ischemic HF (IHF) patients, 8 nonischemic HF patients (NIHF), and 8 healthy volunteers (matched by age and sex - normal controls [NCs]) were chosen for miR sequencing. The plasma RNA was extracted, and a small RNA library of HF was established and then sequenced using next-generation sequencing (NGS) technology. The miR-195-3p was selected for a second clinical study in 60 IHF, 48 NIHF patients, and 35 NCs for qRT-PCR validation. Results: The expression of circulating miR-195-3p in the IHF group was increased 69.5-fold compared with the NC group using NGS technique, and it was the most elevated in all upregulated miRs. MiR-195-3p was ranked in the top 1 of all upregulated miRs in contribution to HF based on a random forest model analysis. The upregulation of circulating miR-195-3p was also validated with the qRT-PCR method, and receiver operating characteristic curve analysis showed that the area under the curve (AUC) was 0.831. Conclusions: The circulating miR-195-3p was upregulated in IHF and NIHF patients and could be a potential biomarker for HF.

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“…This is followed by read mapping and iltering of other RNA sequences (rRNA, tRNA, snRNA, mRNA, lncRNA, etc.). The reads thought to represent miRNA are analyzed with miRNA prediction tools like miRDeep2 [69], miRanalyzer [70], mirTools 2.0 [71], etc. (Table 3).…”

Section: Mirna Processing Stepsmentioning

confidence: 99%

“…These tools can use several features such as sequence conservation among species, structural features like hairpin and minimal folding free energy [72]. Many tools are available for miRNA annotation (htps://tools4mirs.org/software/known_mirna_identiication/) [73] including frequently used tools like miRdeep [74], miRanalyzer [75], mirTools 2.0 [71], UEA sRNA Workbench [76], sRNAtoolbox [77], and SeqBuster [78] ( Table 3). Many more tools have been developed for novel miRNA discovery and miRNA precursor prediction (htps://tools4mirs.org/software/ precursor_prediction/) [73] including frequently used tools like MiPred [79], miRanalyzer [75], miR-Abela [80], MiReNA [81], UEA sRNA Workbench [76] and mirDeep [74] ( Table 3).…”

Section: Tools For Mirna Identiicationmentioning

confidence: 99%

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

Ngoc¹,

Dudemaine²,

Fomenky³

et al. 2017

Applications of RNA-Seq and Omics Strategies - From Microorganisms to Human Health

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The recent remarkable development of transcriptomics technologies, especially next generation sequencing technologies, allows deeper exploration of the hidden landscapes of complex traits and creates great opportunities to improve livestock productivity and welfare. Non-coding RNAs (ncRNAs), RNA molecules that are not translated into proteins, are key transcriptional regulators of health and production traits, thus, transcriptomics analyses of ncRNAs are important for a beter understanding of the regulatory architecture of livestock phenotypes. In this chapter, we present an overview of common frameworks for generating and processing RNA sequence data to obtain ncRNA transcripts. Then, we review common approaches for analyzing ncRNA transcriptome data and present current state of the art methods for identiication of ncRNAs and functional inference of identiied ncRNAs, with emphasis on tools for livestock species. We also discuss future challenges and perspectives for ncRNA transcriptome data analysis in livestock species.

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mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing

Abstract: (2013) mirTools 2.0 for non-coding RNA discovery, profiling, and functional annotation based on high-throughput sequencing, RNA Biology, 10:7,

Cited by 87 publications

References 36 publications

miRNA assays in the clinical laboratory: workflow, detection technologies and automation aspects

miRNA assays in the clinical laboratory: workflow, detection technologies and automation aspects

Upregulation of Circulating miR-195-3p in Heart Failure

Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

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