# The set of scripts reported in this folder are able to reproduce the full
# computational analysis published in:
# Identification of miRNAs potentially involved in Bronchiolitis Obliterans
# Syndrome: a computational study.
#
# This README file provides guidelines for the execution of the scripts and for
# the interpretation of the results
#
# *****************************************************************************
# **** Step 0 LOCAL DATABASES *************************************************
# *****************************************************************************
# To make sure reslults can be reproduced a snapshot of all used databases has
# been created and included in this package.
# *****************************************************************************


# *****************************************************************************
# **** Step 1 AUTOMATIC LITERATURE MINING *************************************
# *****************************************************************************
# Retrieve interesting pathways for BOS by automatic literature mining
#
# Excute:  source literature_mining.sh
#
# Output: results/literature_mining_pathway_list.csv
# The list of identified pathways in CSV format.
# *****************************************************************************



# *****************************************************************************
# **** Step 2 PATHWAY PROCESSING **********************************************
# *****************************************************************************
# Precess the pathways identified in step 1 and saved in the 2-Pathway-List.csv
# file.
#
# Excute:  source 2-Pathway-Processing.sh
#
# Output:
# - one file for each pathway stored in results/processed-pathways/ and
# containing the list of nodes (genes, TF, miRNA) of the pathway
# - Two summary files: results/processed-pathways/pathways-info-targets-all.csv
# and pathways-info-targets-mirtarbase.csv containing the summry information
# of the pathway considering all mirna targets or only targets from mirtarbase
#
# *****************************************************************************



# *****************************************************************************
# **** Step 3 miRNA PROCESSING ************************************************
# *****************************************************************************
# Precess the miRNA to collect data for the miRNA enrichment analysis.
#
# Excute:  source 3-Mirna-Processing.sh
#
# Output:
# - results/mirna_tissue_filtered_mirna_list.csv the list of filtered
# miRNA (by relevant tissue and by host gene)
# - results/mirna-targets-info.csv mirna/pathway target matrix required to
# perform the enrichment analysis
#
# *****************************************************************************


 *****************************************************************************
# **** Step 4 miRNA ENRICHMENT ANALYSIS***************************************
# *****************************************************************************
# Performs the miRNA enrichment analysis and compute mirna scores.
#
# Excute:  source 4-Enrichment-Analisys.sh
#
# Output:
# - results/mirnascore-alltargets.csv the list of scored mirna considering
# all targets
# - results/mirnascore-alltargets.tif a plot of the top 30 scored mirna
# (p<0.01) considering all targets
# - results/mirnascore-mirtarbase.csv the list of scored mirna considering
# mirtarbase targets
# - results/mirnascore-mirtarbase.tif a plot of the top 30 scored mirna
# (p<0.01) considering all mirtarbase
#
# *****************************************************************************