miRNA Target mRNA miRNA Expression Downloads FAQ

Frequently Asked Questions

How can I get a list of all target sites for a gene / all genes targeted for a microRNA / etc.

Why is the energy score always 0 for the Sept2008 downloadable tables?

What expression data is available? Where can I find it?

How do I select multiple tissues for the miRNA expression section?

Can you tell me more information about a tissue in the Expression data?

Why am I getting segmentation faults / buffer overflows when running miRanda?

Where can I get an binary executable of miRanda for my Operating System?

Where can I get post-processing scripts which process output from miRanda

How do I configure miRanda and get it running?

How can I get a list of all target sites for a gene / all genes targeted for a microRNA / etc.

Tables of target predictions can be downloaded from the Downloads tab. These tables are formatted as tab delimited text files.

Why is the energy score always 0 for the Sept2008 downloadable tables?

In older versions of the downloadable tables, the energy was 0 because we stopped using an energy score cutoff for the Sept2008 release. When that release was assembled, we did not compute the energy score. However, we have gone back and recomputed the energy scores and updated the tables. We also made corrections to the miRNA accession ids. So if your download tables from this release has all zeros in the energy column, you may want to download the updated tables from the Downloads page.

What expression data is available? Where can I find it?

Currently, this site allows you to review miRNA expression patterns across the tissues presented in the Landgraf et al. paper. We may add additional expression profiles in the future. You can download the expression tables in tab delimited format from the Downloads page.

How do I select multiple tissues for the miRNA expression section?

To select multiple tissues, hold down the control key (windows) or command key (mac) while clicking on the tissue names with the mouse.

Can you tell me more information about a tissue in the Expression data?

For more detailed descriptions of the tissues presented, refer to A mammalian microRNA expression atlas based on small RNA library sequencing. Landgraf P., et al., Cell 2007 Jun 29;129(7):1401-14.

Why am I getting segmentation faults / buffer overflows when running miRanda?

The most common cause of this problem is attempting to predict targets on overly long input sequences. Inputting the full hairpin precursor sequences instead of the mature microRNA, for example. Or attempting to predict targets across an entire chromosome at once, instead of searching individual UTRs or genes. Using the most recent version of miranda is also a good idea if you are experiencing this problem; the aug2010 version will dynamically allocate memory instead of using a static maximum length for input sequences.

Where can I get an binary executable of miRanda for my Operating System?

We distribtue a source code package for miRanda on the Downloads page. This can be fairly easily configured and built on systems running a Unix-based operating system. For other systems, some porting and system specific configuration will likely be needed. There are some old versions of miRanda in binary executable format here: http://cbio.mskcc.org/miRNA2003/miranda.html. We hope to update that page with executables of more recent miRanda versions.

Where can I get post-processing scripts which process output from miRanda

The scripts we use to process the output of miRanda and generate the additional scores and database structures are not yet ready for distribution. We hope to make these available soon, including explanations and documentation to enable use and adaptation.

How do I configure miRanda and get it running?

The source code distribution available on the Downloads page is designed to be easily installed on a Unix compatible operating system. We use it under Linux and Macintosh OS-X. If you have such a system, you can unpack the tar file with

 tar -xvzf {name_of_miRanda_tarfile}

for example,

 tar -xvzf miRanda-aug2010.tar.gz

Second, you must configure the code for your platform. Change the default directory to the miranda directory and then use:

 ./configure --prefix {directory_to_install_to}

for example,

 ./configure --prefix /Users/yourname/miRanda_aug2010

You may omit the --prefix command to build miranda in the current src directory. If the directory specified with --prefix does not yet exist, the make program will attempt to create it.

Third, execute

 make install

If you did not specify an install directory, you should simply execute

 make

Then you should have the miRanda execuatble available for use.