ArticleNucleic acids research2015
YM500v2: a small RNA sequencing (smRNA-seq) database for human cancer miRNome research.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Memory-promoting function of miR-379-5p attenuates CD8Journal for immunotherapy of cancer · 2025Article
- The RNA world: from experimental laboratory to "in silico" approach. Part 1: User friendly RNA expression databases portals.Reports of practical oncology and radiotherapy : journal of Greatpoland Cancer Center in Poznan and Polish Society of Radiation Oncology · 2024Review
- Signature of miRNAs derived from the circulating exosomes of patients with amyotrophic lateral sclerosis.Frontiers in aging neuroscience · 2023Article
- In Silico Analysis of MicroRNA Expression Data in Liver Cancer.Cancer informatics · 2023Article
- miR-4759 suppresses breast cancer through immune checkpoint blockade.Computational and structural biotechnology journal · 2022Article
- Using bioinformatics approaches to identify survival-related oncomiRs as potential targets of miRNA-based treatments for lung adenocarcinoma.Computational and structural biotechnology journal · 2022Article
- miRNA therapeutics in precision oncology: a natural premium to nurture.Exploration of targeted anti-tumor therapy · 2022Review
- ROS-Responsive miR-150-5p Downregulation Contributes to Cigarette Smoke-Induced COPD via Targeting IRE1Oxidative medicine and cellular longevity · 2022Article
- Systematic identification of clinically relevant miRNAs for potential miRNA-based therapy in lung adenocarcinoma.Molecular therapy. Nucleic acids · 2021Article
- miRge3.0: a comprehensive microRNA and tRF sequencing analysis pipeline.NAR genomics and bioinformatics · 2021Article
- Identification and validation of a miRNA-based prognostic signature for cervical cancer through an integrated bioinformatics approach.Scientific reports · 2020Article
- MirGeneDB 2.0: the metazoan microRNA complement.Nucleic acids research · 2020Article
- DriverDBv3: a multi-omics database for cancer driver gene research.Nucleic acids research · 2020Article
- Simvastatin induces breast cancer cell death through oxidative stress up-regulating miR-140-5p.Aging · 2019Article
- microRNA 92b-3p regulates primordial follicle assembly by targeting TSC1 in neonatal mouse ovaries.Cell cycle (Georgetown, Tex.) · 2019Article
- MicroRNA-139-3p Suppresses Tumor Growth and Metastasis in Hepatocellular Carcinoma by Repressing ANXA2R.Oncology research · 2018Article
- Liquid biopsy and PCR-free ultrasensitive detection systems in oncology (Review).International journal of oncology · 2018Review
- A Comprehensive Approach to Sequence-oriented IsomiR annotation (CASMIR): demonstration with IsomiR profiling in colorectal neoplasia.BMC genomics · 2018Article
- Dicer partner protein tunes the length of miRNAs using base-mismatch in the pre-miRNA stem.Nucleic acids research · 2018Article
- Global DNA methylation analysis reveals miR-214-3p contributes to cisplatin resistance in pediatric intracranial nongerminomatous malignant germ cell tumors.Neuro-oncology · 2018Article
Corrections and comments
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Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We previously presented YM500, which is an integrated database for miRNA quantification, isomiR identification, arm switching discovery and novel miRNA prediction from 468 human smRNA-seq datasets. Here in this updated YM500v2 database (http://ngs.ym.edu.tw/ym500/), we focus on the cancer miRNome to make the database more disease-orientated. New miRNA-related algorithms developed after YM500 were included in YM500v2, and, more significantly, more than 8000 cancer-related smRNA-seq datasets (including those of primary tumors, paired normal tissues, PBMC, recurrent tumors, and metastatic tumors) were incorporated into YM500v2. Novel miRNAs (miRNAs not included in the miRBase R21) were not only predicted by three independent algorithms but also cleaned by a new in silico filtration strategy and validated by wetlab data such as Cross-Linked ImmunoPrecipitation sequencing (CLIP-seq) to reduce the false-positive rate. A new function 'Meta-analysis' is additionally provided for allowing users to identify real-time differentially expressed miRNAs and arm-switching events according to customer-defined sample groups and dozens of clinical criteria tidying up by proficient clinicians. Cancer miRNAs identified hold the potential for both basic research and biotech applications.
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