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is a web-tool that allows to annotate a VCF-file or single position with experimentally confirmed microRNA binding regions (Exp-miBR) and their features.
microRNAs are small noncoding RNAs, that accomplish an essential post-transcriptional regulation of gene expression. Previously, we showed that commonly used microRNA-mRNA interactions predicting software differ from each other substantially, while had a great discrepancy with microRNAs’ binding regions identified in experiments . Experimentally identified microRNA binding regions could be promising as a basis for further queries into not only the fundamental aspects of gene regulation but may uncover some new mechanisms caused diseases.
We have aggregated various experimental data on human microRNA-mRNA interactions to identify reliable microRNA binding regions:
We have extracted from these microRNA binding regions only highly reliable regions (Exp-miBRs) that
had a subsequence of length L=10, whereas each nucleotide (position) in this subsequence had been supported
by at least n=2 different datasets or chimeras.
In total, we revealed 46,8 thousand of experimentally confirmed microRNA binding regions, that were located in all parts of mRNAs, including noncoding regions.
We characterized each Exp-miBR by the following parameters:
There are a few different modes to analyze nucleotide variants location in exp-miBR:
Input vcf file contains the following variants:
SOME HEADINGS #CHROM POS ID REF ALT QUAL FILTER INFO 1 40073961 . . . . . . 3 68194389 . G A . . . 7 43876072 . . . . . .
The output vcf file will be extended by new fields in INFO (to all variants that are located in exp-miBRS) and their descriptions in heading section.
SOME HEADINGS ##INFO=ID=MIRNA_STRAND,Number=.,Type=String,Description="A comma-separated list of miRNAs" ##INFO=ID=MIRNA_NDATASET,Number=.,Type=Integer,Description="Number of datasets" ##INFO=ID=MIRNA_DATASET,Number=.,Type=String,Description="A comma-separated list of datasets" ##INFO=ID=MIRNA_NLINES,Number=.,Type=Integer,Description="Number of cell lines" ##INFO=ID=MIRNA_LINES,Number=.,Type=String,Description="A comma-separated list of cell lines" ##INFO=ID=MIRNA,Number=.,Type=String,Description="A comma-separated list of miRNAs" ##INFO=ID=MIRNA_REGION,Number=.,Type=String,Description="A comma-separated list of region descriptors" ##INFO=ID=MIRNA_GENES,Number=.,Type=String,Description="A comma-separated list of genes" #CHROM POS ID REF ALT QUAL FILTER INFO 1 40073961 . . . . . MIRNA_STRAND=-;MIRNA_NDATASET=3;MIRNA_DATASET=GSE32113%GSM796037,GSE32113%GSM796038,GSE50452%CLASH;MIRNA_NLINES=2;MIRNA_LINES=BC-1,HEK293;MIRNA=hsa-miR-320a;MIRNA_REGION=UTR3;MIRNA_GENES=PPT1 3 68194389 . G A . . . 7 43876072 . . . . . MIRNA_STRAND=-;MIRNA_NDATASET=2;MIRNA_DATASET=GSE28865%GSM714644,GSE28865%GSM714646;MIRNA_NLINES=1;MIRNA_LINES=HEK293;MIRNA_REGION=UTR3;MIRNA_GENES=URGCP
Full information about supported experiments could be find at NCBI GEO by the provided GSE and GSM ids.
Example of input vcf file with correct headings: Example_input.vcf (634B)
Example of output vcf file: Example_output.vcf (2KB)
Download all high confidence microRNA binding regions along with the characteristics of each of these regions as tsv file (reference of human genome: hg19) Exp-miBRS_track_information_hg19.tsv (6,5MB)
Download all high confidence microRNA binding regions along with the characteristics of each of these regions as tsv file (reference of human genome: hg38) Exp-miBRS_track_information_hg38.tsv (6,6MB)
While the paper is under review, please cite pre-print version
Plotnikova, Olga, Ancha Baranova, and Mikhail Skoblov. "Comprehensive analysis of human microRNA-mRNA interactome." bioRxiv (2019): 675694. doi: https://doi.org/10.1101/675694
This tab allows you to submit a single point at a time. While you can make as many of these submissions as you want, if you have more than a dozen of points to process, you should consider the VCF submission form instead.
You can upload and process any VCF file (v4.0-4.2), though your upload can be no more than 20MB. The file can be compressed by any gzip-compatible method (for instance, gzip itself or bgzip). To limit workload, our system only processes the first 500k lines from a submitted VCF file (excluding the header lines). The output is a bgzipped VCF v4 file.