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Exp-miBR annotator

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.


Motivation

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 [1]. 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.


What is exp-miBRs?

We have aggregated various experimental data on human microRNA-mRNA interactions to identify reliable microRNA binding regions:

  • Two existing experiments that had developed and optimized technique protocol to obtain full human microRNA-mRNA interactome: CLASH [2] and CLEAR-CLIP [3].
  • 79 AGO2-CLIP-seq data from 9 different cell lines.

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.


Exp-miBRs features:

We characterized each Exp-miBR by the following parameters:

  • Region information: Genome strand +/- (MIRNA_STRAND), gene name (MIRNA_GENES), type of mRNA part (MIRNA_REGION).
  • Supported dataset characteristics: amount (MIRNA_NDATASET) and list (MIRNA_DATASET) of supported experiments (IDs from www.ncbi.nlm.nih.gov/geo) and their corresponding cell lines (MIRNA_LINES, MIRNA_NLINES).
  • Interacted miRNAs (that were detected in CLASH or CLEAR-CLIP experiment as a part of chimeras): list of interacted microRNAs (if accessible) (MIRNA).

How it works?
Starter on the service:

There are a few different modes to analyze nucleotide variants location in exp-miBR:

  • Process a single point: 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.
  • Process a VCF query: Allow you to 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. Please, check that your vcf file has a correct heading form (you can copy it from example vcf file below).
  • Download track: Allow you to download all exp-miBRs with their characteristics as a separate file. There are separate files for both genome versions (hg19 and hg38). Each line in file is corresponded to one exp-miBR.

Example of processing

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

Interpretation:
  1. Variant chr1 40073961: is located in exp-miBR that was supported in 3 (MIRNA_NDATASET=3) experiments (MIRNA_DATASET=GSE32113%GSM796037,GSE32113%GSM796038,GSE50452%CLASH). These three datasets are corresponded to two different cell lines (MIRNA_NLINES=2; MIRNA_LINES=BC-1,HEK293). There is one known interacted microRNA (MIRNA=hsa-miR-320a). This exp-miBR is located in 3 UTR region (MIRNA_REGION=UTR3) of PPT1 gene (MIRNA_GENES=PPT1).
  2. Variant chr3 68194389: is not located in any exp-miBRs.
  3. Variant chr7 43876072: is located in exp-miBR that was supported in 2 (MIRNA_NDATASET=2) experiments (MIRNA_DATASET= GSE28865%GSM714644,GSE28865%GSM714646). These two datasets are corresponded to only one cell line (MIRNA_NLINES=1;MIRNA_LINES=HEK293). Due to the fact that all supported datasets are AGO-CLIP there is no information about interacted microRNA. This exp-miBR is located in 3 UTR region (MIRNA_REGION=UTR3) of PPT1 gene (MIRNA_GENES=URGCP).

Full information about supported experiments could be find at NCBI GEO by the provided GSE and GSM ids.


Download:

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)


How to cite:

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


Reference:
  1. O.M.Plotnikova, M. Y. Skoblov (2018) Efficiency of the miRNA–mRNA interaction prediction programs, Molecular Biology, 52.3:467–477.
  2. Helwak A. et al. (2013) Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding, Cell, 153.3:654–665.
  3. Moore M. J. et al. (2015) miRNA–target chimeras reveal miRNA 3′-end pairing as a major determinant of Argonaute target specificity, Nature communications, 6:8864.

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.

Download all high confidence microRNA binding regions along with the characteristics of each of these regions as tsv file:

Exp-miBRS_track_information_hg19.tsv (6,5MB)

Exp-miBRS_track_information_hg38.tsv (6,6MB)