TargetExpress

Improving miRNA target prediction with gene expression profiles



Download TargetExpress


We provide the core TargetExpress and the TargetScan, microT-CDS, and MIRZA predictions in independent files.


Core TargetExpress

The Core TargetExpress file contains the main script TargetExpress.pl, 5 human tissue expression profiles and the predictions of TargetScan, microT-CDS, and MIRZA for the predictions used in the TargetExpress paper to allow users to test the functionality. It also includes the libsvn.3.20 library.

Version Released File File size
1.0 Jan 14, 2016 TargetExpress 6,1M


Predictions

The Predictions file includes all human and mouse predictions from TargetScan version 6.2, 2012 (miRBase v17), microT-CDS 2013 (miRBase v18), and MIRZA 2013 (mirBase v21). These will be needed if a user wants to run TargetExpress for any human or mouse miRNA, replicating the full website functionality. You must have all the prediction files (10 parts) in the same folder in order to untar them.

Version Released File File size
1.0 Jan 14, 2016 TargetExpress predictions - part 1 153M
1.0 Jan 14, 2016 TargetExpress predictions - part 2 153M
1.0 Jan 14, 2016 TargetExpress predictions - part 3 153M
1.0 Jan 14, 2016 TargetExpress predictions - part 4 153M
1.0 Jan 14, 2016 TargetExpress predictions - part 5 153M
1.0 Jan 14, 2016 TargetExpress predictions - part 6 153M
1.0 Jan 14, 2016 TargetExpress predictions - part 7 153M
1.0 Jan 14, 2016 TargetExpress predictions - part 8 153M
1.0 Jan 14, 2016 TargetExpress predictions - part 9 153M
1.0 Jan 14, 2016 TargetExpress predictions - part 10 51M

To untar the prediction files run:
cat predictions.tar.gza* | tar xvz



Installation Guide


TargetExpress is a perl script that uses the libsvm library with a minor modification (included in the download). You will need to compile this library before using TargetExpress. To do so, decompress the TargetExpress.tar.gz file and in a Terminal execute the following:

cd TargetExpress
cd libsvm-3.20
make

This command will create the svm-train, svm-scale and svm-predict executables. Then add these executables to your $PATH. For instance, if you have /usr/local/bin in your $PATH, you could copy the executables there:

sudo cp svm-train svm-scale svm-predict /usr/local/bin/


If you want to use a different libsvm version

ONLY If you have previously downloaded libsvm and you want to use your own version, a single line must be added to your original svm.cpp file (http://www.csie.ntu.edu.tw/~cjlin/libsvm/faq.html) before re-compiling.

In a text editor, find the following (should be line 2587):

svm_predict_values(model, x, dec_values);

and add after it:

printf("%f\n", dec_values[0]*model->label[0]);

You can then recompile and install as usual:

make clean
make

Finally you will need to add the new executables svm-train, svm-scale and svm-predict to your $PATH.


Usage


After installing libsvm, go to TargetExpress directory.

cd TargetExpress

You can run TargetExpress as follows:

perl TargetExpress.pl miR_ID TargetScan[1/0] microT-CDS[1/0] MIRZA[1/0] expressionFile outFile

The Core TargetExpress download only contains TargetScan, microT-CDS, and MIRZA for predictions used our TargetExpress paper. If you want to get the complete set of TargetScan, microT-CDS, and MIRZA predictions see the predictions section.

Example

perl TargetExpress.pl hsa-miR-1 1 1 1 tissues/brain.tab brainTargetExpress.tab