By integrating the three best performing algorithms to infer miRNA mediate regulation from co-expression signatures we have constructed a generalizable Framework for Inference of Regulation by miRNAs (FIRM). FIRM is available as a Python script capable of identifying putative miRNA mediated regulation from transcriptome co-expression signatures.
FIRM was developed in Linux, but by ensuring the following dependencies are met could be modified to work in Windows. In order to function properly this script requires:
- Python 2.6 or greater (but less than 3.X) - the lastest python can be downloaded here.
- R - the lastest R can be found here.
- Weeder - the lastest Weeder can be found here. The paths of this must be configured to identify the location of the frequency files packaged with FIRM. A successful installation of Weeder will allow a user to type 'weederlauncher' at the command line and will run the 'weederlauncher.out' program from Weeder 1.4.2.
We provide FIRM as a tarred and gzipped file:
Once downloaded navigate a Linux command prompt to the directory containing the file and run:
prompt> tar xvzf FIRM.tgz
Here is a brief description of the files and folders in the FIRM directory:
prompt> ls FIRM
FIRM.py TargetPredictionDatabases common exp miRvestigator.py pssm.py weeder_FreqFiles
If the dependencies above are met then to run FIRM will simply require the user to create the appropriate co-expression signature files and place them in the 'exp' directory. Then the analysis can be started by typing:
prompt> python FIRM.py
FIRM limits the Weeder-miRvestigator method to only those inferences of miRNA mediated regulation with a perfect 7- or 8-mer miRvestigator complementarity p-value (p-value = 6.1 x 10-5 or 1.5 x 10-5, respectively) to a miRNA seed in miRBase. Inferences of miRNA mediated regulation from the PITA and TargetScan enrichment of predicted miRNA target genes methods were filtered to include only those with Benjamini-Hochberg FDR = 0.001 and at least 10% of genes had a predicted miRNA binding site. After FIRM finished running it will produce a file 'combinedResults.csv' in the main FIRM directory. For the This file will contain a listing of all co-expression signatures that were predicted to be regualted by a miRNA. The column headings are:
- Dataset - the dataset where the co-expression signature was observed.
- signature - nubmer for the co-expression signature.
- miRvestigator.miRNA - miRvestigator predicted miRNA(s).
- miRvestigator.model - model that fit the miRNA to the PSSM found through Weeder, either 7mer or 8mer.
- miRvestigator.mature_seq_ids - the miRBase mature sequence IDs for the predicted miRNAs.
- PITA.miRNA - PITA predicted mirna(s)
- PITA.percent_targets - percent of co-expression cluster genes with predicted target sites in PITA.
- PITA.P_Value - p-value for the hypergeometric enrichment of miRNA(s).
- PITA.mature_seq_ids - the miRBase mature sequence IDs for the predicted miRNAs.
- TargetScan.miRNA - TargetScan predicted mirna(s)
- TargetScan.percent_targets - percent of co-expression cluster genes with predicted target sites in TargetScan.
- TargetScan.P_Value - p-value for the hypergeometric enrichment of miRNA(s).
- TargetScan.mature_seq_ids - the miRBase mature sequence IDs for the predicted miRNAs.