MiRNA
From BITS wiki
A brief chronology of RNAi and miRNA discovery can be found on the RNAi WEB as well as biological mechanism responsible for RNA silencing and other handy resources and references.
Contents
Desktop packages
Databases
miRNA databases
- miRBase - searchable database of published miRNA sequences and annotations, both source as hairpin sequences. Contains a multitude of organisms.
- miRWalk - known miRNAs and predicted and experimentally validated targets and organ distribution. Human, mouse, rat.
- siRecords - experimentally validated animal miRNAs interacting with their targets. Vertebrate and invertebrate animals
miRNA target databases
- miRecords - animal miRNA-target interactions, both predicted and experimentally validated targets.
- miRGator - database and navigator tool for functional interpretation of miRNAs
- Tarbase - experimentally supported miRNA targets.
- microRNA.org - predicted miRNA targets. Human, mouse and rat.
- TargetScanHuman 5.1 - predicted miRNA targets in mammals.
- miRWalk - known miRNAs, and predicted and experimentally validated targets. Human, mouse, rat.
- PicTar - predicted microRNA targets. Vertebrates, insect, nematodes.
- miRGen - integrates widely used target prediction programs, merges miRNAs with genomic annotations.
- miRBase - searchable database of published miRNA sequences and annotations.
- MirtCat - target database, including non-canonical nucleation bulges. human and mouse
miRNA vs genomic variation
- miRSNP - collection of human SNPs in predicted miRNA target sites
- miR-SNPDB - searching and retrieving Single Nucleotide Polymorphisms (SNPs) annotation data in terms of miRNA and mRNA interaction.
- miR2Disease - miRNA deregulation in various human diseases (manually curated).
- miROrho - predicted precursor miRNA genes, with alignments of homologous sequences
miRNA vs gene regulation
- miRStart - database of transcription start sites of miRNA genes
Prediction
Precursor prediction
- MapMi - miRNA precursor prediction in genomic sequences.
- miRAlign - Predicts miRNA precursor (one by one).
- miR-abela - detecting of miRNA precursors in genomic sequences
- RNAmicro - detects miRNA precursors in a list of small non-coding sequences
- miRDeep - detecting miRNAs from NGS data (local installation)
- miRanalyser - detecting miRNAs from NGS data (webinterface)
- SSCprofiler - retrieves miRNA precursors from the human genome.
Target prediction
- DIANA-microT 3.0 - miRNA target prediction, combined with gene expression.
- TargetScan - detects miRNA binding sites in genes, and level of conservation.
- TAPIR - Predicts plant miRNA target genes.
- psRNATarget - Predicts plant miRNA target genes.
Integration
- GeneSet2MiRNA - Translates a gene list into a miRNA regulatory model.
- MMIA - integrates miRNA and mRNA expression data with predicted microRNA target information for analysis with Gene Set Enrichment Analysis (GSEA).
- miRNAMap - miRNA expression profiles from Q-PCR experiments on 224 human miRNAs in 18 major normal tissues in human.
- smirnaDB - expression information of small RNAs (mostly miRNAs) for human, mouse, rat, zebrafish, worm and fruitfly . Clustering and mining tools are also available on the site.
- miRSystem is a database which integrates seven well known miRNA target gene prediction programs: DIANA, miRanda, miRBridge, PicTar, PITA, rna22, and TargetScan.
Abandoned
- miRacle - miRNA target prediction, incorporating RNA secondary structure
- MicroInspector - detects miRNA binding sites, incorporating thermodynamics
