Functional module

Using the IsomiR Window standalone pipeline for the functional module

Step 1 -Download functional.pl to perform miRNA target and gene set enrichment analysis on the set of identified targets

This script performs the following automated analysis: a) target prediction of miRNAs or isomiRs by invoking Miranda and/or TargetScan in the case of animal genomes or by invoking Targetfinder in the case of plant genomes.

In case you have not created as instructed in the Annotation module wiki page, create directory:

/Knowledge_bases --> directory with genome assemblies (fasta and indexed genomes), RNAcentral.gff3 and miRBase.gff and 3'UTR (to receive these knowledge bases please send email to isomiR_window1.0@gmail.com write the species code in subject. Then you will receive a link to transfer all the required files.

/isomiR_list.FASTA--> fasta file with miRNA or isomiR sequences for which mRNA targets are to be predicted

/inputs_to_target_predictor --> in this folder different input files for analysis are created. Input files in the required format for target predictors are generated in an automated manner, final list of mRNA targets that is inputed by TopGo (in case the user selects TargetScan and Miranda a list corresponding to the overlap of the results obtained from these predictors is produced)

**/results --> folder where results obtained from a single target predictor are written as well as the results from the gene set enrichment analysis provided by TopGo

Species code

        Bos_taurus
        Canis_familiaris
        Capra_hircus
        Danio_rerio
        Drosophila_melanogaster
        Equus_caballus
        Gallus_gallus
        Homo_sapiens
        Mus_musculus
        Ovis_aries
        Pan_troglodytes
        Rattus_norvegicus
        Sus_scrofa
        
        Arabidopsis_thaliana
        Brachypodium_distachyon
        Oryza_sativa
        Solanum_lycopersicum
        Sorghum_bicolor
        Vitis_vinifera
        Zea_mays

Requires:

Species.pl

R_topGO.R

targetfinder.pl

targetscan_70.pl 1 =yes 0 =no

perl functional.pl <jobID> <pathto>/Knowledge_bases <pathto>/isomiR_list.FASTA <pathto>/inputs_to_target_predictor <pathto>/results <speciescode>, <TargetScan "1" or "0"> <miRanda "1" or "0"> <targetFinder "1" or "0">