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miRBase Frequently Asked Questions

FAQ Contents

Finding information in miRBase

Downloadable content

Confidence levels

Deep sequencing data

General questions


How can I obtain a list of all the miRNAs for a given species?

Click the 'Browse' tab at the top of the page. The Browse page functions as an expandable list, or 'tree'. By clicking on different taxa, you can expand or collapse each branch of the tree. You can keep expanding the tree until you find the species that you want.

Common model species (human, mouse, fly etc.) can be located quickly using the 'Jump to:' links near the top of the page. You can browse the tree in its entirety by clicking 'Expand all.' Have a go in the window below.

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How many miRNAs are deposited in miRBase for a specific organism?

You can find out how many miRNAs are contained in miRBase for a given organism by finding that specific organism in the 'Browse' feature. When you click on this organism, a table will appear listing all the miRNA entries for that organism. The total is given beside the species name in bold lettering at the top of the page.

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How can I get a list of experiments in miRBase for a given species?

Go to the 'Search' tab, then scroll down to the box entitled 'By tissue expression'. Select the desired species from the first drop-down menu. Leave the tissue drop-down menu blank. Click 'Get experiments.' You are presented with a table containing the experiments performed on your species of choice, each row being a different experiment. Try this out in the window below.

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How can I get a list of miRNAs which are expressed in a specific tissue or cell line?

Go to the 'Search' tab, then scroll down to the box entitled 'By tissue expression'. Select the desired species from the first drop-down menu. From the second drop-down menu, select any of the available tissues or cell lines. Click 'Get experiments' to obtain a table of the experiments which used the organism and tissue/cell line you specified.

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How can I compare miRNA expression levels from different experiments?

First, follow the steps as detailed for the previous question. On the table that you obtain, the right-most column is entitled 'Compare exp.' This column contains a list of check-boxes. Tick all those which correspond to the experiments you want to compare (maximum of five). Scroll to the bottom of your page, and click 'Submit'.You will be presented with a table comparing the miRNA expression levels from the experiments you chose. Please note that this can take a while to load. You can then sort your table according to read count for any of the experiments that you chose by clicking on the table headings. In the window below try comparing some experiments from A. thaliana using the instructions given here.

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How can I find miRNA targets?

Some miRNAs in miRBase have predicted and/or validated target sites. miRBase provides external links to tools which contain information regarding the targets of particular miRNAs. These links can be found on the entry page for that particular miRNA. For example, let's have a look at the miRBase entry for cel-let-7. If we scroll down this miRNA entry page we will see this:

What is this telling us? Well, it shows us that the 5' mature miRNA of cel-let-7 has validated targets, information for which has been deposited in TARBASE, and can be accessed using the corresponding link. We can also see that the 5' mature sequence has predicted targets, details of which are present in three different tools, all of which are accessible by their corresponding links. We can also see that there are two tools providing links to predicted targets of the 3' mature sequence.

Note: not all miRNA entries will have predicted/validated targets. Only the entries that contain the 'Predicted targets' and 'Validated targets' boxes have targets, and hence will have links to external tools.

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Do I need permission to download/use data contained in miRBase for my own research?

No. Because miRBase is in the public domain and is not copyrighted, you may freely modify, redistribute, or use the data for any purpose. To read the full miRBase license, please follow this link. However, if you use any data presented in miRBase, we ask that you cite the articles which are presented on the miRBase homepage in addition to any primary research literature.

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How can I download selected sequences from miRBase for my own research?

In a table of miRNAs, the 'Fetch' column can be used to retrieve sequences. You should tick the 'Fetch' boxes corresponding to the desired miRNAs. Once the desired miRNAs are ticked, they can be obtained by clicking 'Fetch Sequences' at the bottom of the page. Whether you fetch stem-loop sequences or mature sequences, and in what format, depends on the options selected from the drop-down boxes adjacent to the 'Fetch Sequences' button.

Individual stem-loop sequences or mature sequences of single miRNAs can be downloaded using the 'Get sequence' button. This is possible when viewing a specific miRNA entry.

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How can I download a set of all the miRNA sequences belonging to a single species?

You should use the browse feature, accessible via the 'Browse' tab, to select your species of choice. By clicking on your desired species, a table will be returned which lists all the miRNA entries stored in miRBase for that particular species. At the bottom of this table is a button which reads 'Select all'. Click this to select all the miRNA entries in the table. Now, click 'Fetch Sequences'. You will then obtain all the miRNA seqeunces for that particular species. You may choose whether to fetch stem-loop sequences or mature sequences, and choose the file format, by changing the options in the drop-down boxes adjacent to the 'Fetch Sequences' button.

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How can I download all stem-loop sequences and/or all mature miRNA sequences?

Click on the 'Download' tab near the top of the page. This page allows you to access all the downloadable content associated with miRBase. To obtain stem-loop or mature miRNA sequences in FASTA format, click on the 'hairpin.fa' link (for stem-loop sequences) or the 'mature.fa' link (for mature miRNA seqeunces). Your file will be downloaded. Once you have located the download file, you can open it in a plain text editor.

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How can I find the differences between the current miRBase release and the previous miRBase release?

Go to the downloads page by clicking the 'Download' tab at the top of the page. Next, click the link 'miRNA.diff'. This will download the miRNA.diff text file to your Downloads folder. This can then be opened using a plain text editor.

All the changes from the previous release to the current release are listed in this file. You will see that there are three columns. The first column provides the accession numbers of the stem-loop or the mature miRNA sequence. Stem-loops can be distinguished from mature sequences by the structure of their accession numbers. Stem-loop sequence accession numbers are written thus, 'MI0028437', whereas mature miRNA sequences are written thus, 'MIMAT0033018'.

This second column gives the miRNA or mature sequence name which corresponds to the accession number.

The third column gives details of the precise changes that have occured with the corresponding miRNA since the previous release. A key explaining these descriptions is provided at the top of the text file.

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How can I access old releases of miRBase?

Go to the 'Download' tab near the top of the page. Then click the 'Previous releases' link. A small pop-up window will appear. In this window, select 'Connect as: Guest' instead of 'Connect as: Registered User'. Then, click 'Connect'. Another window will appear containing a number of files. Each file corresponds to a release of miRBase - the lower the number, the earlier the release.

When you double-click on your desired release, another window will appear which corresponds to the miRBase release you selected. In this new window, you will see all the files associated with that particular release.

In this example, you can see that we have opted for release 4.0. As a result, all the database files for release 4.0 are presented to us.

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How can I access all the database files?

To create a local copy of the database, you must download all the necessary database files. This is done by clicking the 'Download' tab near the top of the page, and then clicking the 'Go to the FTP site' link. A pop-up requesting a name and password will appear. Instead of 'Registered User', you should select 'Guest'. Click 'Connect'.

You will now be able to see a window containing folders and zip files. Double-click on the folder named 'database_files'. You will then be able to see a window listing all the database files.

When you double-click on any of these files, a copy will be downloaded to the 'Downloads' folder on your computer. Retrieving one or more of these database files allows you to query large miRNA datasets or to recreate the entire database locally.

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How can I find a list of previous miRNA names?

Go to the FTP site, which is accessible by following the steps outlined in the FAQ entitled 'How can I access all the database files?'.

In the 'database_files' folder, double-click on 'miRNA.txt.gz' to download the 'mirna.txt' file into the Downloads folder on your computer. This file contains details of all the miRNAs in miRBase, and previous names are provided in the fourth column where applicable.

Previous names are also given, where applicable, on the corresponding miRNA entry page.

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How can I get a list of intronic miRNAs?

Go to the FTP site, which is accessible by following the steps outlined in the FAQ entitled 'How can I access all the database files?'.

In the 'database_files' folder, double-click the file entitled 'mirna_context.txt.gz'. A file entitled 'mirna_context.txt' will be delivered to the Downloads file on your computer. This can be opened with a plain text editor. Once open, you will see that there are numerous columns corresponding to (left to right): miRNA ID, transcript ID, + or - (according whether the sequence lies on the sense or antisense strand, respectively, of a stem-loop structure), where the miRNA originates (i.e. intron, exon, 5' UTR or 3'UTR), the number of the exon or intron from which the miRNA originates, the transcript source, and the transcript name.

You can now query this table to identify all the miRNAs which originate from introns.

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What are confidence levels?

Confidence levels are a measure of the certainty that a particular miRNA actually exists. A sequence has high confidence if it has at least 10 reads mapping to each arm, or at least 5 reads mapping to each arm and at least 100 reads mapping in total (some well-established, highly expressed miRNAs have a high arm expression bias). You can contribute to confidence levels by voting according to whether you believe a miRNA to be real or not.

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How can I find a high confidence miRNA set for a given species?

First, select your species of choice using the 'Browse' feature. Clicking on your desired species produces a table of all the miRNAs in miRBase for that species. The column second-from-the-right is labelled 'Confidence'. The rows that contain a tick in this column are high confidence miRNAs. A dash denotes low confidence. A list of only high confidence miRNAs is obtained by clicking the 'Show high confidence miRNAs' button at the top-right. Using the window below, try obtaining a list of only the high confidence miRNAs in the complete set of miRNAs for D. melanogaster.

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How can I access deep sequencing data?

Deep sequencing data can be accessed via a miRNA entry page, although not all miRNA entries have deep sequencing data. Clicking on the deep sequencing data for a particular miRNA links you to a page that provides a detailed map of 5' and 3' reads on the stem-loop structure, while also showing a read count and normalisation (mean number of reads per million, RPM). Details of the deep sequencing experiments, and references to the corresponding papers, are also provided.

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What do the deep sequencing diagrams mean?

Deep sequencing diagrams demonstrate where on a stem-loop structure 5' and 3' reads map to. This is depicted by a histogram. The height of a bar for each nucleotide corresponds to the normalised number of nucleotides from different reads mapping to that specific nucleotide. Pink bars indicate nucleotides contained within the mature sequences, whereas blue bars indicate nucleotides lying outside of the mature sequences.

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Why are deep sequencing diagrams not present for every miRNA?

Sometimes, particularly for less well-characterised miRNAs, deep sequencing data is not available. This is due to a lack of deep sequencing data in our database. We are making efforts to provide deep sequencing data for as many miRNAs as possible, but this is still work in progress!

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Why does the deep sequencing read count for a particular miRNA entry differ from the number of reads presented on the corresponding deep sequencing diagram?

The read count for a particular miRNA will initially be greater than the number of reads presented in the deep sequencing diagram because reads containing mismatches are not shown unless specified. Take the below example from cel-mir-8196b (correct at the time of writing):

miRBase is telling us that there are five reads for this miRNA. When we click on this value we see this:

Now, miRBase is showing no reads. Why is this? Because, only perfectly matching reads are displayed. We can reveal all the reads (both matching and partial-mismatching) by scrolling down to the area entitled 'by # mismatches'. Using the drop-down box, select '1' to indicate one mismatch. Next, tick the 'Display untemplated ends' box to allow a greater number of 3' mismatches. Finally, click 'Submit' to see all the reads for that particular miRNA.

We can now see all the reads and where on the stem-loop sequence they map to, along with their read count and normalised count, given as mean number of reads per million.

You can have a go at this for yourself in the window below using mmu-mir-466g.

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How does miRBase obtain deep sequencing data?

Data from deep sequencing experiments is uploaded to miRBase from the Gene Expression Omnibus (GEO). Links to the individual GEO datasets are provided on the 'deep seqeuncing reads' page for a particular miRNA. The example below is a section taken from the cel-let-7 'deep sequencing reads' page.

Each row corresponds to a deep sequencing experiment in which reads for this particular miRNA were sequenced. The experiment datasets from which the reads originated can be found by following the corresponding link in the 'Link' column.

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How many species have miRNA information deposited in miRBase?

The latest release of miRBase, release 21 (June 2014), contains miRNA sequence information from 223 species. These species can be browsed through via the 'Browse' tab at the top of the page.

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How often do you update miRBase?

We aim to update miRBase every six months; however, this schedule is flexible.

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How soon after submission of my sequences will they be available in miRBase?

Your sequences will be available in the public domain in the next miRBase release following publication of your paper describing its discovery.

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Further questions

Please feel free to email mirbase@manchester.ac.uk if you have any further questions.

Alternatively, further information regarding miRBase and miRNA annotation can be found in the following publications:

Further information

miRBase is described in the following articles:

miRBase: integrating microRNA annotation and deep-sequencing data.
Kozomara A, Griffiths-Jones S.
NAR 2011 39(Database Issue):D152-D157

miRBase: tools for microRNA genomics.
Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ.
NAR 2008 36(Database Issue):D154-D158

miRBase: microRNA sequences, targets and gene nomenclature.
Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ.
NAR, 2006, 34, Database Issue, D140-D144

The microRNA Registry.
Griffiths-Jones S.
NAR, 2004, 32, Database Issue, D109-D111

The following publication provides guidelines on miRNA annotation:

A uniform system for microRNA annotation.
Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M, Matzke M, Ruvkun G, Tuschl T.
RNA, 2003, 9(3), 277-279

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