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\title{Reactome Pathway Analysis}
\author{Guangchuang Yu \\
\\
Jinan University, Guangzhou, China}

\begin{document}

\maketitle

<<options,echo=FALSE>>=
options(width=60)
require(ReactomePA)
@

\section{Introduction}

This package is designed for reactome pathway-based analysis. Reactome
is an open-source, open access, manually curated and peer-reviewed
pathway database.

In \Rpackage{ReactomePA}, we plan to implement:
\begin{itemize}
  \item pathway enrichment analysis
  \item gene set enrichment analysis
  \item functional subpathway (active or perturbed subpathway) detection
  \item methods for visualization.
\end{itemize}


\section{Pathway Enrichment Analysis}

Enrichment analysis is a widely used approach to identify biological
themes. Here, we implement hypergeometric model to assess whether the
number of selected genes associated with reactome pathway is larger
than expected. We also implement a category net model for viusalization.

\begin{itemize}
  \item Hypergeometric model

    Hypergeometric model was implemented to assess whether the number
    of selected genes associated with reactome pathway is larger than
    expected.

  \item Category Net Plot

    Category-gene network model was implemented to extract the complex
    relationships between genes and pathways. It provides a high-level
    model to understand the functionalities of genes.

  \item Case Study

    Here, we used a vector of sample entrezgene ID, which was
    converted from an example list of genes from ProfCom
    \url{http://webclu.bio.wzw.tum.de/profcom/examples.php}.

<<load sample data>>=
require(ReactomePA)
data(sample)
sample
x <- enrichPathway(gene=sample,pvalueCutoff=0.05, qvalueCutoff=0.05, readable=T)
head(summary(x))
@

<<<category net plot, eval=F>>=
plot(x, showCategory=5)
@

\begin{figure}[h]
  \begin{center}
    \includegraphics[width=\linewidth]{cnetplot.pdf}
    \caption{Visualization of Pathway enrichment analysis}
    \label{Fig:cnetplot}
  \end{center}
\end{figure}

  \item Compatibal with \Rpackage{clusterProfiler}
    Bioconductor package \Rpackage{clusterProfiler} designed
    visualization for comparing biological themes among gene clusters
    \citep{yu2012}. More details and parameters are described in the
    documentation (Rfunction{?compareCluster}). Figure 2 has been
    generated using the data, as in \cite{yu2012}.
\begin{figure}[h]
  \begin{center}
    \includegraphics[width=.7\linewidth]{rPAclusterProfiler.pdf}
    \caption{Example of working with clusterProfiler package}
    \label{Fig:Pathway Comparison}
  \end{center}
\end{figure}


\end{itemize}

\section{Gene Set Enrichment Analysis}

To be developed.

\section{Session Information}

The version number of R and packages loaded for generating the vignette were:

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\bibliography{ReactomePA}
\end{document}