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miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database

Chih-Hung Chou, Nai-Wen Chang, Sirjana Shrestha, Sheng-Da Hsu, Yu-Ling Lin, Wei-Hsiang Lee, Chi-Dung Yang, Hsiao-Chin Hong, Ting-Yen Wei, Siang-Jyun Tu, Tzi-Ren Tsai, Shu-Yi Ho (+15 others)
2015 Nucleic Acids Research  
These improvements make the miRTarBase one of the more comprehensively annotated, experimentally validated miRNA-target interactions databases and motivate additional miRNA research efforts.  ...  This study describes an update of the miRTar-Base (http://miRTarBase.mbc.nctu.edu.tw/) that provides information about experimentally validated miRNA-target interactions (MTIs).  ...  Finally, miRTarBase is an experimentally validated collection of miRNA-target interactions and is the more updated collection of MTIs, as its content is continually compared with that of previously developed  ... 
doi:10.1093/nar/gkv1258 pmid:26590260 pmcid:PMC4702890 fatcat:zwtequdgofghnc7aaokl3tjr6u

miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database

2019 Nucleic Acids Research  
Owing to the biological significance of miRNAs, miRTarBase was developed to provide comprehensive information on experimentally validated miRNA-target interactions (MTIs).  ...  In conclusion, these improvements promote the miRTarBase as one of the most comprehensively annotated and experimentally validated miRNA-target interaction databases.  ...  Table 1 . 1 List of the databases that are integrated by miRTarBase Type Table 2 . 2 Improvements and the number of miRNA-target interactions with different validation methods provided by miRTarBase  ... 
doi:10.1093/nar/gkz896 pmid:31647101 pmcid:PMC7145596 fatcat:7uduf6co7vd5vjqksdxlhb7isi

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

Chih-Hung Chou, Sirjana Shrestha, Chi-Dung Yang, Nai-Wen Chang, Yu-Ling Lin, Kuang-Wen Liao, Wei-Chi Huang, Ting-Hsuan Sun, Siang-Jyun Tu, Wei-Hsiang Lee, Men-Yee Chiew, Chun-San Tai (+24 others)
2017 Nucleic Acids Research  
In brief, miRTarBase performs a significant role in providing validated experimental data. We believe the release of new version will provide great support in updating the databases mentioned above.  ...  Our database contains validated MTIs that were included in miRGate as experimentally validated data (10) . mirMark is a tool based on machine learning method for miRNA target prediction at the site of  ... 
doi:10.1093/nar/gkx1067 pmid:29126174 pmcid:PMC5753222 fatcat:jh65x2o4knchpfogkerwkz4ije

miRPathDB: a new dictionary on microRNAs and target pathways

Christina Backes, Tim Kehl, Daniel Stöckel, Tobias Fehlmann, Lara Schneider, Eckart Meese, Hans-Peter Lenhof, Andreas Keller
2016 Nucleic Acids Research  
The database contains a large number of miRNAs (2595 human miRNAs), different miRNA target sets (14 773 experimentally validated target genes as well as 19 281 predicted targets genes) and a broad selection  ...  With the database we aim to complement available target pathway web-servers by providing researchers easy access to the information which pathways are regulated by a miRNA, which miRNAs target a pathway  ...  For the experimentally validated sets, we extracted for each miRNA all targets from miRTarBase and used them to create three test sets: (i) MTIs validated by any experimental method, (ii) MTIs validated  ... 
doi:10.1093/nar/gkw926 pmid:27742822 pmcid:PMC5210630 fatcat:uynq2hapkfh6hc2cjkan23v6fu

miRTargetLink—miRNAs, Genes and Interaction Networks

Maarten Hamberg, Christina Backes, Tobias Fehlmann, Martin Hart, Benjamin Meder, Eckart Meese, Andreas Keller
2016 International Journal of Molecular Sciences  
Validated and predicted targets are extracted from databases and an interaction network is presented.  ...  To discover the most relevant biochemical processes influenced by the target network, gene set analysis and miRNA set analysis are integrated.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/ijms17040564 pmid:27089332 pmcid:PMC4849020 fatcat:62g6dabtyjemlkeuhx4bx7c6ja

LimiTT: link miRNAs to targets

Julia Bayer, Carsten Kuenne, Jens Preussner, Mario Looso
2016 BMC Bioinformatics  
The investigation of miRNA target interactions (MTIs) by high throughput screenings is challenging, as frequently used in silico target prediction tools are prone to emit false positives.  ...  Even though DBs exist that contain experimentally validated MTIs, they are limited in their search options and they utilize different miRNA and target identifiers.  ...  Licenses: A TarBase license for usage was included on the LimiTT website. The miRecords authors were informed about our usage of their database as required in their license.  ... 
doi:10.1186/s12859-016-1070-1 pmid:27170328 pmcid:PMC4866021 fatcat:3hsbie5rznegvpwapct3ud53pu

MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis

Valerio Licursi, Federica Conte, Giulia Fiscon, Paola Paci
2019 BMC Bioinformatics  
A reasonable solution is certainly to prioritize miRNA-target interactions to maximize the effectiveness of the downstream analysis.  ...  The statistics is used to assess the significance of an over-representation of miRNA-target interactions and then MIENTURNET filters based on the statistical significance associated with each miRNA-target  ...  It is able to accept as input a list of genes as well as a list of miRNAs searching for both predicted and experimentally validated miRNA-target interactions from the most reliable and updated databases  ... 
doi:10.1186/s12859-019-3105-x pmid:31684860 pmcid:PMC6829817 fatcat:2svntrlohndxzhjl3otbld245i

Predicting miRNA Targets by Integrating Gene Regulatory Knowledge with Expression Profiles

Weijia Zhang, Thuc Duy Le, Lin Liu, Zhi-Hua Zhou, Jiuyong Li, Yun Zheng
2016 PLoS ONE  
Results In this article we present an integrative framework, CIDER (Causal miRNA target Discovery with Expression profile and Regulatory knowledge), to predict miRNA targets.  ...  Our results reveal that even a limited amount of either Transcription Factor (TF)-miRNA or miRNA-mRNA regulatory knowledge improves the performance of miRNA target prediction, and the combination of the  ...  The detailed information of experimentally validated miRNA-mRNA interactions retrieved from all these databases can be found in S3 File. Predicted miRNA-mRNA interaction database.  ... 
doi:10.1371/journal.pone.0152860 pmid:27064982 pmcid:PMC4827848 fatcat:nh5opdzmtzeapc7ovauilqekli

Validated MicroRNA Target Databases: An Evaluation

Yun Ji Diana Lee, Veronica Kim, Dillon C. Muth, Kenneth W. Witwer
2015 Drug development research (Print)  
We evaluated the performance of four databases of experimentally validated miRNA:target interactions (miRWalk 2.0, miRTarBase, miRecords, and TarBase 7.0) using a list of 50 alphabetically consecutive  ...  We examined the provided citations to determine the degree to which each interaction was experimentally supported. To assess stability, we tested at the beginning and end of a five month period.  ...  Acknowledgments The authors thank other members of the Witwer lab for helpful comments and would like to acknowledge funding from several sources.  ... 
doi:10.1002/ddr.21278 pmid:26286669 pmcid:PMC4777876 fatcat:u4r5kp44avha7cdhr5xj42plhi

Increasing the Target Prediction Accuracy of MicroRNA Based on Combination of Prediction Algorithms

Mohammed Q., Mohammad Alhammouri, Kholoud Mukdadi
2016 International Journal of Advanced Computer Science and Applications  
The data mining techniques are used to compare the interactions of miRNA-mRNA that it either belongs to the same gene-family or to different families, and to establish a biological scheme that explains  ...  These attributes can provide an empirical guidance for study of specific miRNA family to scan the whole human genome for novel targets.  ...  The miRTarBase provides the last updated collection compared with other similar miRNA databases.  ... 
doi:10.14569/ijacsa.2016.070653 fatcat:yyobdchsfjenxc3mdh6mmam4ru

IRNdb: the database of immunologically relevant non-coding RNAs

Elena Denisenko, Daniel Ho, Ousman Tamgue, Mumin Ozturk, Harukazu Suzuki, Frank Brombacher, Reto Guler, Sebastian Schmeier
2016 Database: The Journal of Biological Databases and Curation  
The current version of IRNdb documents 12 930 experimentally supported miRNA-target interactions between 724 miRNAs and 2427 immune-related mouse targets.  ...  To facilitate discoveries in ncRNA regulation of immune system-related processes, we developed the database of immunologically relevant ncRNAs and target genes (IRNdb).  ...  Experimentally supported interactions between miRNAs and their target genes were retrieved from two databases: miRTarBase (19) and miRecords (20) .  ... 
doi:10.1093/database/baw138 fatcat:rpouylvdq5ewbi3josjme34l3u

Expanding the horizons of microRNA bioinformatics

Rachael P. Huntley, Barbara Kramarz, Tony Sawford, Zara Umrao, Anastasia Kalea, Vanessa Acquaah, Maria J. Martin, Manuel Mayr, Ruth C. Lovering
2018 RNA: A publication of the RNA Society  
To date, our resource provides over 4400 Gene Ontology annotations associated with over 500 microRNAs from human, mouse, and rat and over 2400 experimentally validated microRNA:target interactions.  ...  We illustrate how this resource can be used to create microRNA-focused interaction networks with a biological context using the known biological role of microRNAs and the mRNAs they regulate, enabling  ...  ACKNOWLEDGMENTS We are very grateful to the GO Consortium for providing the ontology and approving our requests for new terms.  ... 
doi:10.1261/rna.065565.118 pmid:29871895 pmcid:PMC6049505 fatcat:hznyudm7gfccnarijk3ayybcoi

ChemiRs: a web application for microRNAs and chemicals

Emily Chia-Yu Su, Yu-Sing Chen, Yun-Cheng Tien, Jeff Liu, Bing-Ching Ho, Sung-Liang Yu, Sher Singh
2016 BMC Bioinformatics  
The database not only compares gene lists affected by chemicals and miRNAs, but also incorporates curated pathways to identify possible interactions.  ...  Until now, more than 2500 mature miRNAs in human have been discovered and registered, but still lack of information or algorithms to reveal the relations among miRNAs, environmental chemicals and human  ...  Acknowledgements We thank the NTNU BISBE Lab for supporting computational resources for this work.  ... 
doi:10.1186/s12859-016-1002-0 pmid:27091357 pmcid:PMC4836156 fatcat:aobxrhu66nfotl6mugqssbidmi

Identification of potential microRNAs-mediated from sialic acid to MMP-9 pathway through integrative analysis

Negar Noorbakhsh, Mina Zamani, Hamid Galehdari
2020 Network Biology  
Then TARGET SCAN, DIANA-TarBase8, and miRDB database were utilized to predict the miRNAs which have the most effective to target genes.  ...  The twenty-one selected micro-RNAs could be the proper options for experimental studies from sialic acid receptors (siglecs) to MMP-9. Among them miR-34a-5p could be the most interesting target.  ...  Table 1 1 MiRTarBase the experimentally validated microRNA-target interaction database found microRNAs finding from Cytoscape that links to genes in pathway.  ... 
doaj:8d30fda49ee44510bdf31449b06e82cd fatcat:bcvbmc37wreazbymvd5wgqow6i

IRNdb: The database of immunologically relevant non-coding RNAs [article]

Elena Denisenko, Daniel Ho, Ousman Tamgue, Mumin Ozturk, Harukazu Suzuki, Frank Brombacher, Reto Guler, Sebastian Schmeier
2016 bioRxiv   pre-print
The current version of IRNdb documents 12,930 experimentally supported miRNA-target interactions between 724 miRNAs and 2,427 immune-related murine targets.  ...  To facilitate discoveries in ncRNA regulation of immune system-related processes we developed the database of immunologically relevant ncRNAs and target genes (IRNdb).  ...  Acknowledgements This work was supported by the NRF Competitive Programme for Unrated Researchers (CSUR) to RG and SS.  ... 
doi:10.1101/037911 fatcat:euk7kipbwfahrhwdymwppoflsm
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