• miRBase

  • Referenced in 23 articles [sw14367]
  • database is a searchable database of published miRNA sequences and annotation. Each entry ... represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with ... location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences ... available for download. The miRBase Registry provides miRNA gene hunters with unique names for novel...
  • starBase

  • Referenced in 10 articles [sw23121]
  • starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale ... CLIP-Seq data. Although microRNAs (miRNAs), other non-coding RNAs (ncRNAs) (e.g. lncRNAs, pseudogenes ... binding protein binding sites, we identified ∼9000 miRNA-circRNA, 16 000 miRNA-pseudogene ... most comprehensive CLIP-Seq experimentally supported miRNA-mRNA and miRNA-lncRNA interaction networks to date...
  • iMiRNA-PseDPC

  • Referenced in 10 articles [sw22425]
  • pseudo distance-pair composition approach. A microRNA (miRNA) is a small non-coding RNA molecule ... human genome may encode over 1000 miRNAs. Albeit poorly characterized, miRNAs are widely deemed ... regulators of biological processes. Aberrant expression of miRNAs has been observed in many cancers ... important for both basic research and miRNA-based therapy to discriminate the real pre-miRNAs...
  • JIVE

  • Referenced in 12 articles [sw09511]
  • JIVE analysis of gene expression and miRNA data on Glioblastoma Multiforme tumor samples reveals gene ... miRNA associations and provides better characterization of tumor types. par Data and software are available...
  • miRecords

  • Referenced in 6 articles [sw29356]
  • integrated resource for microRNA–target interactions. MicroRNAs (miRNAs) are an important class of small noncoding ... been made in computational target prediction of miRNAs in recent years. More than 10 miRNA ... been established, yet, the prediction of animal miRNA targets remains a challenging task. We have ... developed miRecords, an integrated resource for animal miRNA–target interactions. The Validated Targets component...
  • MiPred

  • Referenced in 5 articles [sw29580]
  • combined features. To distinguish the real pre-miRNAs from other hairpin sequences with similar stem ... loops (pseudo pre-miRNAs), a hybrid feature which consists of local contiguous structure-sequence composition ... MiPred decides whether it is a pre-miRNA-like hairpin sequence ... sequence is a pre-miRNA-like hairpin, the RF classifier will predict whether...
  • miRTarBase

  • Referenced in 4 articles [sw29360]
  • miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database. MicroRNAs (miRNAs) are small ... miRTarBase.mbc.nctu.edu.tw/) that provides information about experimentally validated miRNA-target interactions (MTIs). The latest update ... miRTarBase expanded it to identify systematically Argonaute-miRNA-RNA interactions from 138 crosslinking and immunoprecipitation ... fold since the 2014 miRTarBase update. The miRNA and gene expression profiles from The Cancer...
  • miTarget

  • Referenced in 4 articles [sw27473]
  • using a support vector machine. Background: MicroRNAs (miRNAs) are small noncoding RNAs, which play significant ... posttranscriptional regulators. The functions of animal miRNAs are generally based on complementarity for their ... components. Although several computational miRNA target-gene prediction methods have been proposed, they still have ... support vector machine (SVM) classifier for miRNA target gene prediction. It uses a radial basis...
  • MiRFinder

  • Referenced in 3 articles [sw29577]
  • wide fast microRNA precursor scans. Background: MicroRNAs (miRNAs) are recognized as one of the most ... transcriptional regulators of gene expression. Identification of miRNAs is an important requirement for understanding ... mechanisms of post-transcriptional regulation. Hundreds of miRNAs have been identified by direct cloning ... several species. However, there are still many miRNAs that remain to be identified...
  • ProMiR II

  • Referenced in 3 articles [sw29582]
  • service for the prediction of potential microRNAs (miRNAs) in a query sequence ... using a probabilistic colearning model. Identification of miRNAs requires a computational method to predict clustered ... nonclustered, conserved and nonconserved miRNAs in various species. Here we present an improved version ... identifying new clusters near known or unknown miRNAs. This new version, ProMiR II, integrates additional...
  • miRExpress

  • Referenced in 3 articles [sw29587]
  • supported, efficient and flexible tool for detecting miRNA expression profile. The analysis of two Illumina ... demonstrate the effectiveness of miRExpress to obtain miRNA expression profiles and show the usability ... finding novel miRNAs...
  • NPInter

  • Referenced in 3 articles [sw29361]
  • RNAs (lncRNAs) and other biomolecules (proteins, mRNAs, miRNAs and genomic DNAs). In NPInter v3.0, interactions ... technologies. In addition, we also curated lncRNA–miRNA interactions from in silico predictions supported...
  • mirTools

  • Referenced in 2 articles [sw29588]
  • discovery based on high-throughput sequencing. miRNAs are small, non-coding RNA that negatively regulate ... candidates into known categories, such as known miRNAs, non-coding RNA, genomic repeats and coding ... provide detailed annotation information for known miRNAs, such as miRNA/miRNA*, absolute/relative reads count ... most abundant tag; (v) predict novel miRNAs that have not been characterized before...
  • RNAplex

  • Referenced in 4 articles [sw17143]
  • gene silencing by means of siRNAs and miRNA as well as snoRNA directed RNA editing...
  • RBMMMDA

  • Referenced in 2 articles [sw22491]
  • enables the prediction of multiple types of miRNA-disease associations based on RBMMMDA method. When ... visitors choose a specific disease, potential miRNA associated with this disease based on various association ... shown in a table, where the miRNA name, association type, and potential association probability would...
  • SNPinfo

  • Referenced in 3 articles [sw17360]
  • protein structure, gene regulation, splicing and miRNA binding, and consider whether the alternative alleles...
  • EpimiR

  • Referenced in 1 article [sw29358]
  • database of curated mutual regulation between miRNAs and epigenetic modifications. As two kinds of important ... expression regulators, both epigenetic modification and microRNA (miRNA) can play significant roles in a wide ... many studies have demonstrated that epigenetics and miRNA can affect each other in various ways ... methylation, histone acetylation, H3K4me3, H3S10p) and 617 miRNAs across seven species (including Homo sapiens...
  • DNRLMF-MDA

  • Referenced in 1 article [sw23939]
  • similarities of microRNAs and diseases. Discovering miRNA-disease associations is beneficial to understanding disease mechanisms ... diseases. We all know that discovering the miRNA-disease associations via biological experiments ... cost and high-efficiency way for predicting miRNA-disease associations. In this study, we propose ... method (called DNRLMF-MDA) to predict miRNA-disease associations. DNRLMF-MDA integrates known miRNA-disease...
  • SM2miR

  • Referenced in 1 article [sw29357]
  • microRNA expression. The inappropriate expression of microRNAs (miRNAs) is closely related with disease diagnosis, prognosis ... bioactive small molecules (or drugs) can regulate miRNA expression, which indicates that targeting miRNAs with ... relationships between 151 small molecules and 747 miRNAs in 17 species after manual curation from ... contains the detailed information about small molecules, miRNAs and evidences of their relationships, such...
  • miRNet

  • Referenced in 1 article [sw29355]
  • miRNet - Functional Analysis and Visual Exploration of miRNA–Target Interactions in a Network Context ... gain functional insights into microRNAs (miRNAs), researchers usually look for pathways or biological processes that ... complicated by the fact that a single miRNA can target many genes and multiple miRNAs ... customization, visual exploration and functional interpretation of miRNA–target interaction networks. By integrating multiple high...