---
title: "RTNduals: An R/Bioconductor package for analysis of co-regulatory network motifs and inference of 'dual regulons'."
author: "Vinicius S. Chagas, Clarice S. Groeneveld, Kerstin B. Meyer, A. Gordon Robertson, Mauro A. A. Castro"
date: "`r Sys.Date()`"
bibliography: bibliography.bib
output: BiocStyle::html_document
abstract: Multiple regulators can co-operate or compete to control biological processes. RTNduals is a tool derived from the [RTN](http://bioconductor.org/packages/RTN/) (Reconstruction of Transcriptional Networks) package and searches for possible co-regulatory relationships between pairs of regulators. The tool infers "dual regulon" status, a new concept that tests whether pairs of regulators have similar effects on their sets of target genes (regulons). Members of a pair can be of similar types or different types (e.g. transcription factor (TF)-TF, miRNA-miRNA, TF-miRNA, TF-mRNA). RTN infers interactions between a list of regulators and candidate target gene sets (i.e. regulons) using Mutual Information (MI). The "dual regulon" extension identifies shared targets and assesses the similarity in regulation for these shared targets. RTNduals can identify regulators with shared or opposing effects on cellular phenotypes and can be applied to many different regulatory processes.
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# Overview
Recurrent patterns in biological networks have been termed network motifs [@Bracken2016], which may reflect critical roles in multiple biological processes; for example, regulatory loops between transcription factors and microRNAs [@Zhang2015]. **RTNduals** searches for targets shared between pairs of regulators, using regulatory networks generated by the **RTN package** (for details, please refer to the [RTN documentation](http://bioconductor.org/packages/RTN/)) [@Castro2016]. In such a network, each regulator has an associated set of gene targets (i.e. a regulon), and when we assess the shared targets in the regulons of a pair of regulators, we find that each shared target may be regulated in a positive or negative direction by a given regulator (i.e. pairs of regulators can either agree or disagree on the predicted downstream effects for a shared target gene). 'Dual regulons' represent regulon pairs whose common targets are likely to be affected by both regulators. The inference of 'dual regulons' requires three complementary statistics: (1) Targets are assigned to regulons based on MI between the regulator and the target. The significance of the MI statistics is assessed by permutation and bootstrap analysis. The association between pairs of regulators is also identified in this step, since regulators can target each other. (2) Shared targets between any two regulons are identified and the similarity in regulation (i.e. positive or negative direction) is assessed by correlation analysis. Single network motifs are identified in this step consisting of two regulators and one common target. (3) A test is carried out to determine if the correlation between the set of network motifs of any two regulons is higher than would be expected by chance. The schematics in **Figure 1** show examples of 'dual regulons' with two network motifs each. In (a) the two regulators agree on the downstream effects (i.e. same directions), while in (b) they disagree (i.e. opposite directions). Our method can be applied to any regulatory relationship. For gene expression data sets typical regulators might include transcription factors, miRNAs, eRNAs and lncRNAs.
# Quick Start
The **RTNduals** workflow starts with a preprocessing step that generates an **MBR-class** (Motifs Between Regulons) object from an expression matrix and two lists of regulators. The expression matrix is typically obtained from multiple samples (e.g. transcriptomes from a cancer cohort), while the lists of regulators represent some prior biological information indicating which genes in the expression matrix should be regarded as regulators. The input data can also deal with two classes of regulators; for example, genes and microRNAs. In this case, the expression matrix should comprise mRNA and miRNA expression values. Alternatively, the **MBR-class** object can be obtained by combining two **TNI-class** objects pre-computed in the **RTN** package.
## Load datasets
This example provides the data required to generate an **MBR-class** object. The dataset **dt4rtn** is available from the **RTN** package and consists of an R list with 6 objects, 3 of which will be used in the subsequent analysis: (1) **gexp**, a named gene expression matrix with 250 samples (genes in rows, samples in cols), (2) **gexpIDs**, a data.frame with Probe-to-ENTREZ annotation, and (3) **tfs**, a named vector listing transcription factors (in this case, 149 TFs). While these datasets were extracted, pre-processed and size-reduced from @Fletcher2013 and @Curtis2012, they should be regarded as examples for demonstration purposes only.
```{r include=FALSE}
library(RTNduals)
data("dt4rtn", package = "RTN")
gexp <- dt4rtn$gexp
annot <- dt4rtn$gexpIDs
tfs1 <- dt4rtn$tfs[c("IRF8","IRF1","PRDM1","AFF3","E2F3")]
tfs2 <- dt4rtn$tfs[c("HCLS1","STAT4","STAT1","LMO4","ZNF552")]
```
```{r eval=FALSE}
##--- load package and prepare a dataset for demonstration
library(RTNduals)
data("dt4rtn", package = "RTN")
gexp <- dt4rtn$gexp
annot <- dt4rtn$gexpIDs
tfs1 <- dt4rtn$tfs[c("IRF8","IRF1","PRDM1","AFF3","E2F3")]
tfs2 <- dt4rtn$tfs[c("HCLS1","STAT4","STAT1","LMO4","ZNF552")]
```
## Preprocessing
The **gexp** data matrix and the corresponding annotation are evaluated by the `mbrPreprocess` function in order to check the consistency of the input data. After this step it is generated a pre-processed **MBR-class** object whose status is updated to 'Preprocess [x]'.
```{r eval=TRUE}
##--- generate a pre-processed BR-class object
rmbr <- mbrPreprocess(gexp=gexp, regulatoryElements1=tfs1, regulatoryElements2=tfs2, gexpIDs=annot, verbose=FALSE)
rmbr
```
## Run permutation analysis
The `mbrPermutation` method inherits the same algorithm implemented in the **RTN** package. This function takes the pre-processed **MBR-class** object and returns two regulatory networks that are inferred by mutual information analysis (with multiple hypothesis testing corrections). The results are included in the 'TNI' slots, which will be used in the subsequent steps of the pipeline.
```{r eval=TRUE}
##--- compute two regulatory networks
##--- (set nPermutations>=1000)
rmbr <- mbrPermutation(rmbr, nPermutations=100, verbose=FALSE)
rmbr
```
## Run bootstrap analysis
In additional to the permutation analysis, the stability of the regulatory networks is assessed by bootstrapping using the `mbrBootstrap` function, which also inherits the same algorithm from the **RTN** package. Each 'TNI' slot of the **MBR-class** object is updated with a consensus bootstrap network.
```{r eval=TRUE}
##--- check the stability of the two regulatory networks
##--- (set nBootstrap>=100)
rmbr <- mbrBootstrap(rmbr, nBootstrap=10, verbose=FALSE)
rmbr
```
## Run DPI filter
In a given regulatory network each target can be linked to multiple regulators as a result of both direct and indirect interactions. The Data Processing Inequality (DPI) algorithm [@Meyer2008] is used to remove the weakest interaction between two regulators and a common target. This step inherits the algorithm that is implemented in the **RTN** package, and it is optional for the analyses described in this workflow (the results of this step can be used to assess regulon activity in the **RTN** package).
```{r eval=TRUE}
##---apply DPI algorithm
rmbr <- mbrDpiFilter(rmbr, eps=0.05, verbose=FALSE)
rmbr
```
## Run association analysis between regulons
The `mbrAssociation` method takes the two transcriptional networks computed in the previous steps and enumerates all motifs between all regulons. The method retrieves the mutual information between regulators and assesses the agreement between the predicted downstream effects using correlation analysis. A hypergeometric test is used to evaluate whether the common targets are potentially affected by both regulators in a number greater than expected by chance. Note that this example warns the user that only a few regulon pairs are being tested. This warning is to recall that the search space should ideally represent all possible combinations of a given class of regulators (for example, all nuclear receptors annotated for a given species).
```{r eval=TRUE}
##--- run the main RTNduals methods
rmbr <- mbrAssociation(rmbr, prob=0.75, verbose=FALSE)
```
A summary of the results can be accessed from the 'summary' slot using the `mbrGet` function.
```{r eval=TRUE}
##--- check summary
mbrGet(rmbr, what="summary")
```
## Rank 'dual regulons'
The `mbrDuals` method ranks all candidates using the correlation values computed in the `mbrAssociation` step, and returns the list of 'dual regulons'.
```{r eval=TRUE}
##--- run 'mbrDuals' and get results
rmbr <- mbrDuals(rmbr)
results <- mbrGet(rmbr, what="dualsInformation")
```
Also, when prior evidences are available this method can add a 'supplementaryTable' regarding the association between regulators. The 'supplementaryTable' is a 'data.frame' listing unique relationships between any two regulators used to compute the 'dual regulons' (please refer to the documentation for details on the input data format).
```{r eval=TRUE}
##--- here we build a 'toy' evidence table using the 'rnorm' function
supplementaryTable <- results[ ,c("Regulon1","Regulon2")]
supplementaryTable$ToyEvidence <- rnorm(nrow(results))
supplementaryTable
```
```{r eval=TRUE}
##--- add supplementary evidences with the 'mbrDuals' function
rmbr <- mbrDuals(rmbr, supplementaryTable = supplementaryTable,
evidenceColname = "ToyEvidence", verbose = FALSE)
```
```{r eval=TRUE}
##--- check updated results
mbrGet(rmbr, what="dualsInformation")
```
## Visualize shared cloud of targets
The package provides the `mbrPlotDuals` function to visualize 'dual regulon' and the respective motifs, which represent the shared cloud of targets. **Figure 2** shows two examples of 'dual regulons' for the schematics illustrated in **Figure 1**. In **(a)** the two regulators agree on the downstream effect (i.e. same directions), while in **(b)** they disagree (i.e. opposite directions).
```{r eval=FALSE}
duals <- mbrGet(rmbr, what="dualRegulons")
mbrPlotDuals(rmbr, names.duals = duals[1])
```
# Session Info
```{r}
sessionInfo()
```
# References