MechRNA is a computational tool for integration RNA-RNA interactions, RNA-Protein interactions and correlation data in order to infer potential mechanisms for a lncRNA of interest.

1. Ensure you have the required dependancies:

   • IntaRNA2 >= 2.2.0
   • Python (tested with version 2.7 and 3.5) with packages:
     • numpy
     • scipy
     • statsmodels
     • configparser (Python2 only)

2. Clone or download MechRNA:

    git clone https://github.com/BackofenLab/mechRNA.git
   

3. Download the required data into /mechrna/data/ which can found here. The file structure should be as shown below:

    /mechrna/data/
    /mechrna/data/correlation/
    /mechrna/data/peaks/
    /mechrna/data/refs/
   

   For screening mode, please also download the correlation file for your cancer type of interest. This file should be placed in the /mechrna/data/correlations/ folder.

You can use

python mechrna.py -h

to get a description of each parameter. For more details, please check doc/MechRNA_manual.pdf (coming soon).

To create a new hypothesis-driven mode project: specify (1) project name and (2) lncRNA transcript ID (3) Files listing the targets, rbps, and mechanisms you are intested in (all are used if not specified):

python mechrna.py -p my_project -l ENSTXXXXXXXXXXX -a [-T my_targets] [-B my_rbps] [-M my_mechanisms]

To create a new screening mode project: specify (1) project name and (2) lncRNA transcript ID (3) correlation file:

python mechrna.py -p my_project -l ENSTXXXXXXXXXXX -c ./data/correlation/correl.genenet.[cancer_type].tcga	

The hypothesis-driven mode parameters can also be specified for screening mode. Screening mode is computationally expensive and should be executed with multiple workers [--num-worker] and ideally on a cluster [--mode slurm/sge/pbs].

Feel free to change my_project to any name you want. The TSV file with the prediction results will be generated in my_project.

This is the validation case from Gawronski et. al (DOI: 10.1093/bioinformatics/bty208)

To run MechRNA on this lncRNA, type the following when in the mechrna root directory:

python mechrna.py -p my_project -l ENST00000618786 -a -T ./example/7SL.ids -M ./example/7SL.mechs

Feel free to drop any inquiry to agawrons at sfu dot ca.