New version of miRWalk is online. Follow this link here.
NEWS
15.02.2016 - Information on validated miRNA-target interactions updated (mirTarBase v6.0) (miRTarBase)
29.04.2015 - Information on validated miRNA-target interactions (Rdata and GSEA files) is integrated.(Click Here)
29.04.2015 - Information on validated miRNA-target interactions on KEGG pathways is integrated.(Click Here)
29.04.2015 - Information on validated miRNA-target interactions on WikiPathways is integrated.(Click Here)
29.04.2015 - Information on validated miRNA-target interactions on PantherDB pathways is integrated.(Click Here)
29.04.2015 - Information on validated miRNA-target interactions on GOBP, GOMF, GOCC is integrated.(Click Here)
29.04.2015 - Information on validated miRNA-target interactions on gene- and protein-classes is integrated.(Click Here)
29.04.2015 - Information on validated miRNA-target interactions on disease- and human phenotype-ontologies is integrated.(Click Here)
21.04.2015 - Information of the Validated Target module is corrected and updated.
How to cite miRWalk2.0?
How to cite miRWalk2.0?
Dweep, H et al. miRWalk - database: prediction of possible miRNA binding sites by "walking" the
genes of 3 genomes, Journal of Biomedical Informatics, 44: 839-7 (2011). (JBIPubMed)
Dweep, H et al. miRWalk2.0: a comprehensive atlas of microRNA-target interactions, Nature Methods, 12(8): 697-697 (2015). (Nature Methods, Pubmed)
miRWalk2.0
is an improved version of the previous database (i.e. miRWalk). miRWalk2.0 is so far the only freely accessible,
comprehensive archive, supplying the biggest available collection of predicted and experimentally verified miRNA-target interactions
with various novel and unique features (missing in a previous version i.e. miRWalk) to greatly assist the miRNA research community.
miRWalk2.0 not only documents miRNA binding sites within the complete sequence of a gene,
but also combines this information with a comparison of binding sites resulting
from 12 existing miRNA-target prediction programs
(DIANA-microTv4.0,
DIANA-microT-CDS,
miRanda-rel2010,
mirBridge,
miRDB4.0,
miRmap,
miRNAMap,
doRiNA i.e.,PicTar2,
PITA,
RNA22v2,
RNAhybrid2.1 and
Targetscan6.2)
to build novel comparative platforms of binding sites for the promoter (4 prediction datasets),
cds (5 prediction datasets), 5’- (5 prediction datasets) and 3’-UTR (13 prediction datasets) regions.
It also documents experimentally verified miRNA-target interaction information collected via
an automated text-mining search and data from existing resources
(miRTarBase,
PhenomiR,
miR2Disease and
HMDD) offer such information.
miRWalk2.0 novelties are as follows:
It hosts possible binding site interaction information (including "central pairing sites")
between genes (encompassing the complete sequence as well as mitochondrial genomes) and
miRNAs resulting from the miRWalk algorithm by walking with a heptamer (7nts)
seed of miRNA from positions 1 to 6.
These different starting positions are considered because
it has recently been identified that miRNAs also regulate the expression of their target genes
by annealing from nucleotides 4 to 15 (PMID:20620952).
13 miRNA-target prediction datasets are documented to upgrade the comparative platform of miRNA binding sites within mRNA 3’-UTR region.
Novel comparative platforms of miRNA binding sites are implemented for the promoter,
5’-UTR and CDS regions by locally executing 5 miRNA-target prediction programs.
A comparative platform of miRNA binding sites on mitochondrial genomes is also integrated.
Recently, it has been suggested that miRNAs can also base-pair with other miRNAs (PMID:14730015).
Therefore, miRWalk2.0 not only offers miRNA-miRNA interactions,
but also combines this information with a comparison of binding sites resulting from 4 prediction algorithms: miRanda, PITA, RNAhybrid and Targetscan.
It provides possible interactions between miRNAs and genes associated with 597 KEGG, 456 Panther and 522 Wiki pathways.
It hosts miRNA binding site interactions on 18,394 gene ontology terms.
It offers miRNA binding sites on gene and protein classes.
Information on miRNA-target interactions on 2,035 disease ontologies (DO),
6,727 Human Phenotype ontologies (HPO) and 4,980 OMIM disorders is available.
A comprehensive atlas is implemented to supply a comparative overview of human homologous genes,
their classes, pathways and ontologies among 15 species.
One can also obtain miRNAs which are significantly enriched for their binding sites within the genes associated with pathways, ontologies and classes.
To foster large-scale enrichment analysis, a novel feature named “Customized datasets” is
implemented through which users can generate a customized list of putative targets on their
miRNAs of interest from 13 different data-sets for promoter, CDS, 5’- and/or 3’-UTR regions.
It provides genomic location search functionality for genes to determine which of miRNA(s) share
the same or nearby location – as previous studies suggest that several mammalian miRNA genes are
co-expressed with their host-gene and/or neighboring genes by utilizing their transcriptional machinery
and promote synergistic and/or antagonistic effects on them (PMID:20370903).
All result pages are presented with links for the gene and miRNAs,
allowing users to retrieve data including miRNA binding sites predicted with different
combination of algorithms, basic information (genes, synonymous, identifiers, definition, mRNAs, etc.),
genomic location (ContigID, chromosome, strand, map, gene start and end positions),
epigenomics, pathways, ontologies, protein classes.
Moreover, external links (such as UniGene, HGNC, OMIM, Ensembl, miRBase, Gene, PubMed, UCSC,
AceView, DGV, CCDS, ClinVar, dbVar, PheGenl, GeneMania, EST, Probe, CDD, GEO, ProteomicDB,
HPM and UniProt) are provided to obtain data on phenotype, genotype, SNPs, splice junction,
functional networks, neighboring genomic members, expressions of genes and proteins in human organs,
their MS/MS spectra and relevant PubMed articles
It also supplies experimentally verified miRNA-target interactions.
The web-interface of miRWalk2.0 is broadly classified into the Predicted Target (PTM) and the Validated Target (VTM) modules.These two modules are further categorized into different search pages, allowing users to fetch miRNA associated information using different identifiers.
The Predicted Target module hosts miRNA-target interactions information within the complete sequence of
all known genes of human, mouse and rat including all transcripts and mitochondrial genomes.
It also provides novel comparative platforms of miRNA binding sites resulting from 13 data-sets for promoter, cds, 5'-, and 3'-UTR, mitochondrial genes and
miRNA-miRNA interactions. miRBase release 20 is utilized to generated miRNA-target interaction information for this module.
The Validated Target module hosts experimentally verified miRNA interaction information associated with genes, pathways, organs, diseases,
cell lines, OMIM disorders and literature on miRNAs. This module is last updated on 29th September 2014.
In addition, it provides the information on proteins known to be involved in miRNA processing.
