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\begin{document}
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\title{\Rpackage{mirIntegrator}: Integrating miRNAs into signaling pathways}
\author{Diana Diaz and Sorin Draghici\\
Department of Computer Science,
Wayne State University,
Detroit MI 48201}
\date{June 9, 2015}
\maketitle

\begin{abstract}

\Rpackage{mirIntegrator} is an R package for integrating microRNAs (miRNAs) into
signaling pathways to perform pathway analysis using both mRNA and miRNA 
expressions. 
Typical pathway analysis methods help to investigate which pathways are 
relevant to a particular phenotype understudy. 
The input of these methods are the fold change of mRNA of two different 
phenotypes 
(e.g. control versus disease), and a set of signaling pathways.
Researchers investigating miRNA cannot perform pathway analysis using traditional 
methods because current
pathways datasets do not contain miRNA-gene interactions.
\Rpackagev{mirIntegrator} aims to fill this gap by:
\begin{enumerate}
\item Integrating miRNAs into signaling pathways, 
\item Generating a graphical representation of the augmented pathways, and
\item Facilitating the use of pathway analysis techniques when studying miRNA and
mRNA expression levels. 
\end{enumerate}

\end{abstract}


\section{Integration of miRNA into signaling pathways}

The main functionality of the \Rpackagev{mirIntegrator} is the integration of
miRNAs into signaling pathways.
The input of this functionality are a set of signaling pathways like KEGG 
pathways \cite{Kanehisa:2000} 
or Reactome \cite{croft2014reactome},
and a miRNA-target interaction database like mirTarBase
\cite{hsu_mirtarbase_2014} 
or TargetScan \cite{lewis:2005b}.
The output is a set of augmented signaling pathways.
Each augmented pathway contains the original sets of genes and interactions plus 
the set of miRNAs involved in the pathways and their miRNA-target interactions.
These interactions are the biological miRNA repression to their target genes and 
are represented in the model as negative interactions. 


Here we show an example of the method functionality. Let us say that some 
researchers
need to 
integrate 
KEGG \cite{Kanehisa:2000}
human signaling pathways with miRNA interactions from miRTarBase
 \cite{hsu_mirtarbase_2014}. 
Researchers must first obtain the list of pathways as a list of 
\Rclass{graph::graphNEL} 
objects. The nodes of each pathway represent the genes involved in the pathway
and the edges represent the biological interactions among those genes
(activation or repression).
The second step is to obtain a miRNA-target interactions dataset as 
a \Rclass{data.frame} with the columns \Robject{"miRNA"} and 
\Robject{"Target.ID"}. Notice that the symbols used to 
identify the \Robject{"Target.ID"} column on the miRNA-target interactions dataset must be the same symbols 
used on the nodes of the pathways. 
i.e. If the genes are identified by entrezID on the pathways' dataset, then
the miRNA-targets dataset must identify the genes by entrezID as well.
Once the researchers have these two datasets, they can use the function 
\Rfunction{$integrate\_mir$}. 


To demonstrate this functionality, \Rpackagev{mirIntegrator} includes the object
\Robject{mirTarBase} which is a copy of
the experimentally validated miRNA-target interactions database 
miRTarBase \cite{hsu_mirtarbase_2014}. 
We downloaded the miRTarBase database 
from \url{http://mirtarbase.mbc.nctu.edu.tw/}
on April 1st, 2015. A complete script describing how this database was downloaded 
and 
formated is included in this package on 
'/inst/scripts/get\_mirTarBase.R'. 


Here an example of how researchers can generate the list of augmented pathways 
from 
five KEGG pathways 
and mirTarBase interactions using the function \Rfunction{$integrate\_mir$}:

<<<eval=TRUE, echo=FALSE>>=
 set.seed(42L)
@ 

%s1
<<eval=TRUE, echo=TRUE>>=
 require("mirIntegrator")
 data(kegg_pathways)
 data(mirTarBase)
 kegg_pathways <- kegg_pathways[18:20] #delete this for augmenting all pathways.
 augmented_pathways <- integrate_mir(kegg_pathways, mirTarBase)
 head(augmented_pathways)
@



The result is a list of pathways where each pathway is a \Robject{graph::graphNEL} 
object. 
When researchers need to see the details of a particular pathway, they can do
so by simply using the KEGG pathway id of the pathway of interest.
For example, the pathway "path:hsa04122" can be reach with the following 
instruction:
%s2
<<eval=TRUE, echo=TRUE>>=
 augmented_pathways$"path:hsa04122"
@

\section{Graphical output}

\Rpackage{mirIntegrator} incorporates a functionality to produce a graphical 
representation of the 
final pathways. This is useful when researchers need to visualize the nodes that 
were added 
to the pathway.
For instance, if they need 
to see how the
pathway of "Sulfur relay system" (path:hsa04122) has changed,
they can plot the augmented pathway using the function 
\Rfunction{plot\_augmented\_pathway}. Here an example, 
Figure \ref{fig:comp} is the output of these instructions:

%s3
<<eval=TRUE, echo=TRUE>>=
  data(names_pathways)
plot_augmented_pathway(kegg_pathways$"path:hsa04122", 
                       augmented_pathways$"path:hsa04122",
                       names_pathways["path:hsa04122"] )
@


\begin{figure}
\centering
<<echo=FALSE, fig=TRUE>>=
  plot_augmented_pathway(kegg_pathways$"path:hsa04122", 
                         augmented_pathways$"path:hsa04122",
                         names_pathways["path:hsa04122"] )
@
\caption{\label{fig:comp}Visualization of the Sulfur relay system augmented
 pathway using the function \Rfunction{plot\_augmented\_pathway}.}
\end{figure}


Another useful function is \Rfunction{plot\_change} which can
be used to see how much the order of the pathways have changed.
To demonstrate this functionality, the \Rpackagev{mirIntegrator} includes a 
copy of
KEGG human signaling pathways.
We obtained these KEGG pathways using the \Rpackagev{ROntoTools}  
\cite{voichitaROntoTools}. A complete script describing how this dataset was obtained is included in this package on 
'/inst/scripts/get\_kegg\_pathways.R'. 
Here an example of the use of the function \Rfunction{plot\_change}. The result is 
shown on Figure \ref{fig:change}:

%s4
<<eval=TRUE, echo=TRUE>>=
  data(augmented_pathways)
  data(kegg_pathways)
  data(names_pathways)
  plot_change(kegg_pathways,augmented_pathways, names_pathways)
@

\begin{figure}
\centering
<<echo=FALSE, fig=TRUE,  height=3, width=6>>=
  plot_change(kegg_pathways,augmented_pathways, names_pathways, sizeT = 10)
@
\caption{\label{fig:change}Plotting of the change of pathways' order using the function \Rfunction{plot\_change}.}
\end{figure}

This package also includes a function to generate of a pdf file 
with the plots of the list of augmented pathways. Here an example of this 
functionality:

%s5
<<eval=TRUE, echo=TRUE>>=
  data(augmented_pathways)
  data(kegg_pathways)
  data(names_pathways)
  pathways2pdf(kegg_pathways[18:20],augmented_pathways[18:20],
               names_pathways[18:20], "three_pathways.pdf")
@


\section{Pathway analysis of miRNA and mRNA: a case study}

The main purpose of the pathways augmentation process is to analyze miRNA and mRNA 
expressions at the 
same time. For this reason, we show here
how to analyze a multiple sclerosis dataset using
the \Rpackagev{mirIntegrator}.
The dataset that we analyzed was published by Jernas, 
M., et. al. \cite{jernas_microrna_2013} whom collected heparin-anticoagulated 
peripheral blood from 21 multiple 
sclerosis (MS) patients and nine healthy controls. Ten of the 21 samples were used 
to profiled mRNA expression, and the 11 
remaining were used to profiled miRNA expression. These datasets are accessible 
at 
NCBI GEO database \cite{edgar_gene_2002} with accession GSE43592. We preprocessed 
the datasets using the \Rpackagev{limma} 
\cite{smyth2005limma}. 
For demonstration purposes, we included the preprocessed datasets on this package.

%s6
<<eval=TRUE, echo=TRUE>>=
  data(GSE43592_miRNA)
  data(GSE43592_mRNA)
@

Once researchers have the data and the augmented pathways, they can run the pathway 
analysis method that they prefer. We suggest to use \Rpackagev{ROntoTools} 
\cite{voichitaROntoTools} because it takes in account the topology of the 
pathways (the method implemented on \Rpackage{ROntoTools} is explained on 
\cite{voichita_incorporating_2012}). 
We 
show here how to perform impact pathway analysis 
\cite{voichita_incorporating_2012} using the
\Rpackagev{ROntoTools} with our augmented pathways:

%s7
<<eval=TRUE, echo=TRUE>>=
  require(graph)
  require(ROntoTools)
  data(GSE43592_mRNA)
  data(GSE43592_miRNA)
  data(augmented_pathways)
  data(names_pathways)
  lfoldChangeMRNA <- GSE43592_mRNA$logFC
  names(lfoldChangeMRNA) <- GSE43592_mRNA$entrez
  
  lfoldChangeMiRNA <- GSE43592_miRNA$logFC
  names(lfoldChangeMiRNA) <- GSE43592_miRNA$entrez
  
  keggGenes <- unique(unlist( lapply(augmented_pathways,nodes) ) )
  interGMi <- intersect(keggGenes, GSE43592_miRNA$entrez)
  interGM <- intersect(keggGenes, GSE43592_mRNA$entrez)
  ## For real-world analysis, nboot should be >= 2000
  peRes <- pe(x= c(lfoldChangeMRNA, lfoldChangeMiRNA ),
              graphs=augmented_pathways, nboot = 200, verbose = FALSE)
  message(paste("There are ", length(unique(GSE43592_miRNA$entrez)),
                "miRNAs meassured and",length(interGMi), 
                "of them were included in the analysis."))
  message(paste("There are ", length(unique(GSE43592_mRNA$entrez)),
                "mRNAs meassured and", length(interGM),
                "of them were included in the analysis."))
  
  summ <- Summary(peRes)
  rankList <- data.frame(summ,path.id = row.names(summ))
  tableKnames <- data.frame(path.id = names(names_pathways),names_pathways)
  rankList <- merge(tableKnames, rankList, by.x = "path.id", by.y = "path.id")
  rankList <- rankList[with(rankList, order(pAcc.fdr)), ] 
  head(rankList)
@

\section{Citing mirIntegrator}

The algorithms and methods for integrating miRNA and mRNA included on this 
package are in publication process. 
\nocite{*}


\bibliographystyle{ieeetr} 
\bibliography{mirIntegrator}


\end{document}
