YM500: a small RNA sequencing (smRNA-seq) database for microRNA research

Cheng, Wei‐Chung; Chung, I‐Fang; Huang, Tse‐Shun; Chang, Shih-Ting; Sun, Hsin‐Yun; Tsai, Chun‐Kuang; Liang, Mindy; Wong, Tai-Tong; Wang, Hsei‐Wei

doi:10.1093/nar/gks1238

Cited by 62 publications

(57 citation statements)

References 60 publications

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“…Small RNA fractions were sequenced using the Illumina GAIIx System (Illumina) following the manufacturer's standard procedure. Sequencing data were analyzed by a published in-house bioinformatics pipeline [16]. The pipeline was conducted to process mRNA contamination, identify known miRNA quantification, and carry out format conversion.…”

Section: Methodsmentioning

confidence: 99%

Dysregulation of Vascular Endothelial Growth Factor Receptor-2 by Multiple miRNAs in Endothelial Colony-Forming Cells of Coronary Artery Disease

Chiu

et al. 2017

J Vasc Res

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Background/Aims: Endothelial colony-forming cells (ECFCs) have the potential to be used in regenerative medicine. Dysfunction of ECFCs is correlated with the onset of cardiovascular disorders, especially coronary artery disease (CAD). Binding of vascular endothelial growth factor A (VEGFA) to vascular endothelial growth factor receptor-2 (VEGFR2) triggers cell motility and angiogenesis of ECFCs, which are crucial to vascular repair. Methods: To identify the miRNA-VEGFR2-dependent regulation of ECFC functions, ECFCs isolated from peripheral blood of disease-free and CAD individuals were subjected to small RNA sequencing for identification of anti-VEGFR2 miRNAs. The angiogenic activities of the miRNAs were determined in both in vitro and in vivo mice models. Results: Three miRNAs, namely miR-410-3p, miR-497-5p, and miR-2355-5p, were identified to be upregulated in CAD-ECFCs, and VEGFR2 was their common target gene. Knockdown of these miRNAs not only restored the expression of VEGFR2 and increased angiogenic activities of CAD-ECFCs in vitro, but also promoted blood flow recovery in ischemic limbs in vivo. miR-410-3p, miR-497-5p, and miR-2355-5p could serve as potential biomarkers for CAD detection as they are highly expressed in the plasma of CAD patients. Conclusions: This modulation could help develop new therapeutic modalities for cardiovascular diseases and other vascular dysregulated diseases, especially tumor angiogenesis.

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Section: Methodsmentioning

confidence: 99%

Dysregulation of Vascular Endothelial Growth Factor Receptor-2 by Multiple miRNAs in Endothelial Colony-Forming Cells of Coronary Artery Disease

Chiu

et al. 2017

J Vasc Res

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“…Previously, we developed the YM500 database (21,22), a database that contains more than 8000 cancer-related smRNA data sets and includes analysis pipelines for novel miRNA prediction, arm switching discovery, isomiR identification and miRNA quantification from smRNA-seq. The previous version of this database focused only on miRNAs.…”

Section: Introductionmentioning

confidence: 99%

YM500v3: a database for small RNA sequencing in human cancer research

Chung¹,

Chang

Chen³

et al. 2016

Nucleic Acids Res

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We previously presented the YM500 database, which contains >8000 small RNA sequencing (smRNA-seq) data sets and integrated analysis results for various cancer miRNome studies. In the updated YM500v3 database (http://ngs.ym.edu.tw/ym500/) presented herein, we not only focus on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). There is growing knowledge of the role of sncRNAs in gene regulation and tumorigenesis. We have also incorporated >10 000 cancer-related RNA-seq and >3000 more smRNA-seq data sets into the YM500v3 database. Furthermore, there are two main new sections, ‘Survival' and ‘Cancer', in this updated version. The ‘Survival’ section provides the survival analysis results in all cancer types or in a user-defined group of samples for a specific sncRNA. The ‘Cancer’ section provides the results of differential expression analyses, miRNA–gene interactions and cancer miRNA-related pathways. In the ‘Expression’ section, sncRNA expression profiles across cancer and sample types are newly provided. Cancer-related sncRNAs hold potential for both biotech applications and basic research.

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“…However, these datasets were obtained by different groups and each of them studied miRNAs in one or a few tissues and diseases. Except for a few databases, such as miRGator v3.0, microRNA.org and YM500, which show the miRNA expression level based on smRNA-seq data, [10][11][12] there are still very few integrative studies which would facilitate further researches. A comprehensive analysis of the current available smRNA-seq data will be very helpful in exploring tissue or disease specific miRNA markers and uncovering the expression of different miRNA variants.…”

Section: Introductionmentioning

confidence: 99%

“…miRNA editing is found to be an evolutionarily conserved mechanism and regulates target mRNA selection and silencing efficiency. 15,16 The YM500 database also provides information about miRNA isoforms and arm switching discovery, 12 however, there are very few comprehensive miRNA editing analysis in different tissues and diseases.…”

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of human small RNA sequencing data provides insights into expression profiles and miRNA editing

Gong

Zhang

et al. 2014

RNA Biology

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MicroRNAs (miRNAs) play key regulatory roles in various biological processes and diseases. A comprehensive analysis of large scale small RNA sequencing data (smRNA-seq) will be very helpful to explore tissue or disease specific miRNA markers and uncover miRNA variants. Here, we systematically analyzed 410 human smRNA-seq datasets, which samples are from 24 tissue/disease/cell lines. We tested the mapping strategies and found that it was necessary to make multiple-round mappings with different mismatch parameters. miRNA expression profiles revealed that on average ∼70% of known miRNAs were expressed at low level or not expressed (RPM < 1) in a sample and only ∼9% of known miRNAs were relatively highly expressed (RPM > 100). About 30% known miRNAs were not expressed in all of our used samples. The miRNA expression profiles were compiled into an online database (HMED, http://bioinfo.life.hust.edu.cn/smallRNA/). Dozens of tissue/disease specific miRNAs, disease/control dysregulated miRNAs and miRNAs with arm switching events were discovered. Further, we identified some highly confident editing sites including 24 A-to-I sites and 23 C-to-U sites. About half of them were widespread miRNA editing sites in different tissues. We characterized that the 2 types of editing sites have different features with regard to location, editing level and frequency. Our analyses for expression profiles, specific miRNA markers, arm switching, and editing sites, may provide valuable information for further studies of miRNA function and biomarker finding.

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YM500: a small RNA sequencing (smRNA-seq) database for microRNA research

Cited by 62 publications

References 60 publications

Dysregulation of Vascular Endothelial Growth Factor Receptor-2 by Multiple miRNAs in Endothelial Colony-Forming Cells of Coronary Artery Disease

Dysregulation of Vascular Endothelial Growth Factor Receptor-2 by Multiple miRNAs in Endothelial Colony-Forming Cells of Coronary Artery Disease

YM500v3: a database for small RNA sequencing in human cancer research

Comprehensive analysis of human small RNA sequencing data provides insights into expression profiles and miRNA editing

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