From BITS wiki
- 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
- 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.
- 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.
- 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.
- miRacle - miRNA target prediction, incorporating RNA secondary structure
- MicroInspector - detects miRNA binding sites, incorporating thermodynamics