PTC

PTC R package contains functions to determine causal miRNAs-mRNA relationships. Detailed information can be found in:

A Pseudo-Temporal Causality Approach to Identifying miRNA-mRNA Interactions During Biological Processes Andres M. Cifuentes-Bernal, Vu VH Pham, Xiaomei Li, Lin Liu, Jiuyong Li, Thuc Duy Le bioRxiv 2020.07.07.192724; doi: https://doi.org/10.1101/2020.07.07.192724

Experiments implemented in our paper can be found in ints/PTC.MainApplication.R

Introduction

Inspired by the pseudo-time concept we develop a novel approach, called the pseudo-time causality (PTC) based approach, to elucidate the miRNA-mRNA interactions during biological processes, using gene expression data with the expression profiles of matched miRNAs and mRNAs in the same cells or samples. Given a biological process, PTC firstly transforms the matched miRNA and mRNA single cell gene expression data to pseudo-time data using the marker genes of the biological process. PTC relies on the causal invariance property (Peters et al., 2015; Pfister et al., 2018) to find the causal relationships between miRNAs andmRNAs from the pseudo-time data.

We have applied PTC to the single cell dataset from Wang et al., 2019 and the bulk data from Pham et al., 2019. In both cases, VIM, an EMT marker, is used to define the pseudo-time. The results have shown that PTC significantly outperforms the benchmark methods in identifying experimentally confirmed miRNA-mRNA interactions using either single cell or bulk data. The results suggest that the temporal information during a biological process is useful for revealing the miRNA-mRNA interactions characterising the biological process.

Installation

PTC runs in the R statistical computing environment. R version 3.6.1 or higher and Bioconductor version 3.11 or higher are required.

1. Please install Bioconductor, you can use the following code in R

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.17")

2. Install Bioconductor dependencies required by PTC

BiocManager::install(c('miRBaseConverter', 'CancerSubtypes'))

3. Install PTC package from github repository

devtools::install_github('AndresMCB/PTC')

Documentation

Detailed information about the functions implemented in PTC can be found in the user manual

Please find the datasets employed in our paper in the folder data