ArticleDatabase : the journal of biological databases and curation2015
MtiBase: a database for decoding microRNA target sites located within CDS and 5'UTR regions from CLIP-Seq and expression profile datasets.
Article in Database : the journal of biological databases and curation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- FOXO1 in cancer: context-dependent roles, microRNA regulation, and therapeutic opportunities.Discover oncology · 2026Review
- miR-34-5p mediates 20E-induced autophagy in the fat body of Bombyx mori by targeting Atg1.BMC genomics · 2025Article
- Gallic Acid Alleviates Glucolipotoxicity-Induced Nephropathy by miR-709-NFE2L2 Pathway in db/db Mice on a High-Fat Diet.Journal of agricultural and food chemistry · 2024Article
- On the rules of engagement for microRNAs targeting protein coding regions.Nucleic acids research · 2023Article
- The MicroRNA Ame-Bantam-3p Controls Larval Pupal Development by Targeting the Multiple Epidermal Growth Factor-like Domains 8 Gene (International journal of molecular sciences · 2023Article
- Bioinformatic Tools for the Identification of MicroRNAs Regulating the Transcription Factors in Patients with β-Thalassemia.Bioinformatics and biology insights · 2022Review
- miRNA therapeutics in precision oncology: a natural premium to nurture.Exploration of targeted anti-tumor therapy · 2022Review
- MicroRNA-mRNA Networks in Pregnancy Complications: A Comprehensive Downstream Analysis of Potential Biomarkers.International journal of molecular sciences · 2021Review
- Article
- Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins.High-throughput · 2019Article
- Comprehensive analysis of miRNA profiles reveals the role of Schistosoma japonicum miRNAs at different developmental stages.Veterinary research · 2019Article
- Overview of microRNA-199a Regulation in Cancer.Cancer management and research · 2019Review
- A mixed antagonistic/synergistic miRNA repression model enables accurate predictions of multi-input miRNA sensor activity.Nature communications · 2018Article
- RNA-binding protein AUF1 suppresses miR-122 biogenesis by down-regulating Dicer1 in hepatocellular carcinoma.Oncotarget · 2018Article
- Role of miR-483 in digestive tract cancers: from basic research to clinical value.Journal of Cancer · 2018Review
- miRNAs target databases: developmental methods and target identification techniques with functional annotations.Cellular and molecular life sciences : CMLS · 2017Review
- miR-2478 inhibits TGFβ1 expression by targeting the transcriptional activation region downstream of the TGFβ1 promoter in dairy goats.Scientific reports · 2017Article
- Interferons Induce Expression of SAMHD1 in Monocytes through Down-regulation of miR-181a and miR-30a.The Journal of biological chemistry · 2017Article
- Combination of AAV-TRAIL with miR-221-Zip Therapeutic Strategy Overcomes the Resistance to TRAIL Induced Apoptosis in Liver Cancer.Theranostics · 2017Article
- Tools for Sequence-Based miRNA Target Prediction: What to Choose?International journal of molecular sciences · 2016Review
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Authors and funding
6 authors.
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Abstract
MicroRNAs (miRNAs) play an important role in the regulation of gene expression. Previous studies on miRNA functions mainly focused on their target sites in the 3' untranslated regions (UTRs) of mRNAs. However, increasing evidence has revealed that miRNAs can also induce mRNA degradation and mediate translational repression via complementary interactions with the coding sequence (CDS) and 5'UTR of mRNAs. In this study, we developed a novel database, MtiBase, to facilitate the comprehensive exploration of CDS- and 5'UTR-located miRNA target sites identified from cross-linking immunoprecipitation sequencing (CLIP-Seq) datasets and to uncover their regulatory effects on mRNA stability and translation from expression profile datasets. By integrating 61 Argonaute protein-binding CLIP-Seq datasets and miRNA target sites predicted by five commonly used programs, we identified approximately 4 400 000 CDS-located and 470 000 5'UTR-located miRNA target sites. Moreover, we evaluated the regulatory effects of miRNAs on mRNA stability and translation using the data from 222 gene expression profiles, and 28 ribosome-protected fragment sequencing, and six pulsed stable isotope labeling with amino acids in culture. Finally, the effects of SNPs on the functions of miRNA target sites were systematically evaluated. Our study provides a useful tool for functional studies of miRNAs in regulating physiology and pathology. Database URL: http://mtibase.sysu.edu.cn.
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