miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions

doi:10.1093/nar/gkx1067

. 2018 Jan 4;46(D1):D296-D302.

doi: 10.1093/nar/gkx1067.

miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions

Chih-Hung Chou^{1

2}, Sirjana Shrestha², Chi-Dung Yang^{2

3}, Nai-Wen Chang⁴, Yu-Ling Lin^{2

5}, Kuang-Wen Liao^{2

6}, Wei-Chi Huang^{1

2}, Ting-Hsuan Sun², Siang-Jyun Tu¹, Wei-Hsiang Lee^{2

7}, Men-Yee Chiew², Chun-San Tai², Ting-Yen Wei⁸, Tzi-Ren Tsai², Hsin-Tzu Huang², Chung-Yu Wang⁶, Hsin-Yi Wu⁶, Shu-Yi Ho², Pin-Rong Chen⁶, Cheng-Hsun Chuang⁶, Pei-Jung Hsieh², Yi-Shin Wu², Wen-Liang Chen², Meng-Ju Li^{2

9}, Yu-Chun Wu², Xin-Yi Huang², Fung Ling Ng², Waradee Buddhakosai², Pei-Chun Huang¹⁰, Kuan-Chun Lan⁶, Chia-Yen Huang^{2

11}, Shun-Long Weng^{12

13

14}, Yeong-Nan Cheng¹, Chao Liang¹, Wen-Lian Hsu¹⁵, Hsien-Da Huang^{1

2

16

17}

Affiliations

¹ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
² Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
³ Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 350, Taiwan.
⁴ Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 106, Taiwan.
⁵ Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, 300, Taiwan.
⁶ Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan.
⁷ Clinical Research Center, Chung Shan Medical University Hospital, Taichung, 402, Taiwan.
⁸ Interdisciplinary Program of Life Science, National Tsing Hua University, Hsinchu, 300, Taiwan.
⁹ Department of Pediatrics, National Taiwan University Hospital Hsinchu Branch, Hsinchu, 300, Taiwan.
¹⁰ Delivery Room, Department of Nursing, National Taiwan University Hospital Hsinchu Branch, Hsinchu, 300, Taiwan.
¹¹ Gynecologic Cancer Center, Department of Obstetrics and Gynecology, Cathay General Hospital, Taipei, 106, Taiwan.
¹² Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, 300, Taiwan.
¹³ Mackay Medicine, Nursing and Management College, Taipei, 112, Taiwan.
¹⁴ Department of Medicine, Mackay Medical College, New Taipei City, 252, Taiwan.
¹⁵ Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan.
¹⁶ Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong Province, 518172, China.
¹⁷ School of Science and Engineering, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong Province, 518172, China.

PMID: 29126174
PMCID: PMC5753222
DOI: 10.1093/nar/gkx1067

miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions

Chih-Hung Chou et al. Nucleic Acids Res. 2018.

. 2018 Jan 4;46(D1):D296-D302.

doi: 10.1093/nar/gkx1067.

Authors

Affiliations

¹ Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.
² Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.
³ Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 350, Taiwan.
⁴ Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 106, Taiwan.
⁵ Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, 300, Taiwan.
⁶ Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan.
⁷ Clinical Research Center, Chung Shan Medical University Hospital, Taichung, 402, Taiwan.
⁸ Interdisciplinary Program of Life Science, National Tsing Hua University, Hsinchu, 300, Taiwan.
⁹ Department of Pediatrics, National Taiwan University Hospital Hsinchu Branch, Hsinchu, 300, Taiwan.
¹⁰ Delivery Room, Department of Nursing, National Taiwan University Hospital Hsinchu Branch, Hsinchu, 300, Taiwan.
¹¹ Gynecologic Cancer Center, Department of Obstetrics and Gynecology, Cathay General Hospital, Taipei, 106, Taiwan.
¹² Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, 300, Taiwan.
¹³ Mackay Medicine, Nursing and Management College, Taipei, 112, Taiwan.
¹⁴ Department of Medicine, Mackay Medical College, New Taipei City, 252, Taiwan.
¹⁵ Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan.
¹⁶ Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong Province, 518172, China.
¹⁷ School of Science and Engineering, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong Province, 518172, China.

PMID: 29126174
PMCID: PMC5753222
DOI: 10.1093/nar/gkx1067

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs of ∼ 22 nucleotides that are involved in negative regulation of mRNA at the post-transcriptional level. Previously, we developed miRTarBase which provides information about experimentally validated miRNA-target interactions (MTIs). Here, we describe an updated database containing 422 517 curated MTIs from 4076 miRNAs and 23 054 target genes collected from over 8500 articles. The number of MTIs curated by strong evidence has increased ∼1.4-fold since the last update in 2016. In this updated version, target sites validated by reporter assay that are available in the literature can be downloaded. The target site sequence can extract new features for analysis via a machine learning approach which can help to evaluate the performance of miRNA-target prediction tools. Furthermore, different ways of browsing enhance user browsing specific MTIs. With these improvements, miRTarBase serves as more comprehensively annotated, experimentally validated miRNA-target interactions databases in the field of miRNA related research. miRTarBase is available at http://miRTarBase.mbc.nctu.edu.tw/.

PubMed Disclaimer

Figures

**Figure 1.**
Overall system flow of miRTarBase. miRTarBase aims to be a more comprehensive database of experimentally verified miRNA-targets interaction. This database was released in 2011. The current database contains more than 420,000 MTIs.

**Figure 2.**
Top 10 Human miRNAs, genes, and diseases with strong evidence of MTIs in miRTarBase.

**Figure 3.**
Natural language processing (NLP) techniques for identifying MTI articles. (1) Collecting Articles from public literature database, PubMed; (2) detecting sentence boundary of each abstract; (3) preprocessing articles in the following steps; split sentences, tokenization, stemming and stopword removal; (4) Named Entity Recognition (NER) based on statistical principle-based approach (SPBA), Conditional Random Fields (CRFs) and dictionary-based approach; (5) all sentences will be labeled as labeled sentences for principle matching; (6) following construction and evaluation of model, an inference engine for MTI extraction was developed in SPBA; (7) the inference engine is constructed for assist domain exports to manually check the generated positive principles (the * element is not required, e.g., experiment); (8) all curated articles were manually evaluated by biological domain experts.

See this image and copyright information in PMC

Cited by

An integrative network-based approach to identify driving gene communities in chronic obstructive pulmonary disease.
Marino R, El Aalamat Y, Bol V, Caselle M, Del Giudice G, Lambert C, Medini D, Wilkinson TMA, Muzzi A. Marino R, et al. NPJ Syst Biol Appl. 2024 Oct 26;10(1):125. doi: 10.1038/s41540-024-00425-6. NPJ Syst Biol Appl. 2024. PMID: 39461973 Free PMC article.
Role of Circulating microRNAs in Liver Disease and HCC: Focus on miR-122.
Colaianni F, Zelli V, Compagnoni C, Miscione MS, Rossi M, Vecchiotti D, Di Padova M, Alesse E, Zazzeroni F, Tessitore A. Colaianni F, et al. Genes (Basel). 2024 Oct 12;15(10):1313. doi: 10.3390/genes15101313. Genes (Basel). 2024. PMID: 39457437 Free PMC article. Review.
MicroRNA Inhibiting Atheroprotective Proteins in Patients with Unstable Angina Comparing to Chronic Coronary Syndrome.
Kowara M, Kopka M, Kopka K, Głowczyńska R, Mitrzak K, Kim DA, Sadowski KA, Cudnoch-Jędrzejewska A. Kowara M, et al. Int J Mol Sci. 2024 Oct 2;25(19):10621. doi: 10.3390/ijms251910621. Int J Mol Sci. 2024. PMID: 39408950 Free PMC article.
Next-Cell Hypothesis: Mechanism of Obesity-Associated Carcinogenesis.
Engin AB, Engin A. Engin AB, et al. Adv Exp Med Biol. 2024;1460:727-766. doi: 10.1007/978-3-031-63657-8_25. Adv Exp Med Biol. 2024. PMID: 39287871 Review.
MicroRNAs Regulate the Expression of Genes Related to the Innate Immune and Inflammatory Response in Rabbits Infected with Lagovirus europaeus GI.1 and GI.2 Genotypes.
Ostrycharz-Jasek E, Fitzner A, Siennicka A, Budkowska M, Hukowska-Szematowicz B. Ostrycharz-Jasek E, et al. Int J Mol Sci. 2024 Sep 2;25(17):9531. doi: 10.3390/ijms25179531. Int J Mol Sci. 2024. PMID: 39273479 Free PMC article.

See all "Cited by" articles

References

1. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004; 116:281–297. - PubMed
1. Chen D., Farwell M.A., Zhang B.. MicroRNA as a new player in the cell cycle. J. Cell. Physiol. 2010; 225:296–301. - PubMed
1. Shivdasani R.A. MicroRNAs: regulators of gene expression and cell differentiation. Blood. 2006; 108:3646–3653. - PMC - PubMed
1. Lima R.T., Busacca S., Almeida G.M., Gaudino G., Fennell D.A., Vasconcelos M.H.. MicroRNA regulation of core apoptosis pathways in cancer. Eur. J. Cancer. 2011; 47:163–174. - PubMed
1. Kozomara A., Griffiths-Jones S.. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014; 42:D68–D73. - PMC - PubMed

Publication types

Actions

MeSH terms

Actions
Actions
Actions
Actions
Actions
Actions
Actions

Substances

Actions
Actions

LinkOut - more resources

Full Text Sources
Other Literature Sources

[1] Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004; 116:281–297. - PubMed

[2] Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004; 116:281–297. - PubMed

[3] Chen D., Farwell M.A., Zhang B.. MicroRNA as a new player in the cell cycle. J. Cell. Physiol. 2010; 225:296–301. - PubMed

[4] Chen D., Farwell M.A., Zhang B.. MicroRNA as a new player in the cell cycle. J. Cell. Physiol. 2010; 225:296–301. - PubMed

[5] Shivdasani R.A. MicroRNAs: regulators of gene expression and cell differentiation. Blood. 2006; 108:3646–3653. - PMC - PubMed

[6] Shivdasani R.A. MicroRNAs: regulators of gene expression and cell differentiation. Blood. 2006; 108:3646–3653. - PMC - PubMed

[7] Lima R.T., Busacca S., Almeida G.M., Gaudino G., Fennell D.A., Vasconcelos M.H.. MicroRNA regulation of core apoptosis pathways in cancer. Eur. J. Cancer. 2011; 47:163–174. - PubMed

[8] Lima R.T., Busacca S., Almeida G.M., Gaudino G., Fennell D.A., Vasconcelos M.H.. MicroRNA regulation of core apoptosis pathways in cancer. Eur. J. Cancer. 2011; 47:163–174. - PubMed

[9] Kozomara A., Griffiths-Jones S.. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014; 42:D68–D73. - PMC - PubMed

[10] Kozomara A., Griffiths-Jones S.. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014; 42:D68–D73. - PMC - PubMed

Save citation to file

Email citation

Add to Collections

Add to My Bibliography

Your saved search

Create a file for external citation management software

Your RSS Feed

miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions

Affiliations

miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions

Authors

Affiliations

Abstract

Figures

Similar articles

Cited by

References

Publication types

MeSH terms

Substances

LinkOut - more resources

Full Text Sources

Other Literature Sources