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