\section{Figures from the paper}\label{Figures}
In this section all figures from the original publication are shown. In the next
sections the \R{} code for the analysis is documented. A link to the respective 
section in which the figure is generated is given for each figure.

\begingroup
\parindent=0pt

\begin{minipage}[t]{0.5\textwidth}
  \subsection*{Figure 1cd}
  \R{} code for this figure is documented in Section~\ref{exampleSingleKDPhenotypes}.
  \begin{center}
    \includegraphics[width=0.4\textwidth]{result/Figures/singleKnockDown-SETD8.pdf}
    \includegraphics[width=0.4\textwidth]{result/Figures/singleKnockDown-TCF20.pdf}
  \end{center}
\end{minipage}
\begin{minipage}[t]{0.5\textwidth}
  \subsection*{Figure 2a}
  \R{} code for this figure is documented in Section~\ref{QControlFeatures}.
  \begin{center}
    \includegraphics[width=0.7\textwidth]{result/Figures/QCscatterFeaturesBetweenReplicates.pdf}
  \end{center}
\end{minipage}

\begin{minipage}[t]{0.33\textwidth}
  \subsection*{Figure 2bd}
  \R{} code in Section~\ref{QControlFeatures} and \ref{QControlGenes}.
  \begin{center}
    \includegraphics[width=0.7\textwidth]{result/Figures/QCreproducibilityOfFeatures.pdf}
    \includegraphics[width=0.7\textwidth]{result/Figures/QCreproducibilityOfTargetsiRNA.pdf}
  \end{center}
\end{minipage}
\begin{minipage}[t]{0.33\textwidth}
  \subsection*{Figure 2c}
  \R{} code in Section \ref{QControlGenes}.
  \begin{center}
    \vspace{5ex}
    \includegraphics[width=0.5\textwidth]{result/Figures/QCreproducibilityOfTargetsiRNAexample.pdf}
  \end{center}
\end{minipage}
\begin{minipage}[t]{0.33\textwidth}
  \subsection*{Figure 2e}
  \R{} code in Section \ref{smallCellNumber}.
  \begin{center}
    \vspace{10ex}
    \includegraphics[width=0.8\textwidth]{result/Figures/subsamplingNrInteractions.pdf}
  \end{center}
\end{minipage}

\begin{minipage}[t]{0.5\textwidth}
  \subsection*{Figure 3ab}
  \R{} code for this figure is documented in Section \ref{exampleDoubleKDPhenotypes}.
  \begin{center}
    \includegraphics[width=0.4\textwidth]{result/Figures/interaction-PHF16-SETD8.pdf}
    \includegraphics[width=0.4\textwidth]{result/Figures/interaction-SIN3A-RUVBL1.pdf}
  \end{center}
\end{minipage}
\begin{minipage}[t]{0.5\textwidth}
  \subsection*{Figure 3c}
  \R{} code for this figure is documented in Section \ref{OverlapOfInteractions}.
  \begin{center}
<<VennDiagram>>=
# load(file.path("result","Figures","Overlap.rda"))
# print(Overlap)
@
  \end{center}
\end{minipage}

\begin{minipage}[t]{0.5\textwidth}
  \subsection*{Figure 4ac}
  \R{} code for this figure is documented in Section \ref{heatmaps}.
  \begin{center}
    \includegraphics[width=0.4\textwidth]{result/Figures/heatmapAll.pdf}
    \includegraphics[width=0.45\textwidth]{result/Figures/heatmapSelection.pdf}
  \end{center}
\end{minipage}
\begin{minipage}[t]{0.5\textwidth}
  \subsection*{Figure 4b}
  \R{} code for this figure is documented in Section \ref{siRNAcorrelation}.
  \begin{center}
    \vspace{2ex}
    \includegraphics[width=0.9\textwidth]{result/Figures/multidensityWithinDesignCorrelation.pdf}
  \end{center}
\end{minipage}

\begin{minipage}[t]{\textwidth}
  \subsection*{Figure S3}
  \R{} code for this figure is documented in Section \ref{featureSelection}.
  \begin{center}
    \includegraphics[width=0.4\textwidth]{result/Figures/FeatureSelectionInformationgain.pdf}
    \includegraphics[width=0.4\textwidth]{result/Figures/FeatureSelectionRatioPositive.pdf}
  \end{center}
\end{minipage}

\begin{minipage}[t]{\textwidth}
  \subsection*{Figure S4}
  \R{} code for this figure is documented in Section \ref{heatpairsFeatures}.
  \begin{center}
    \includegraphics[width=0.6\textwidth]{result/Figures/heatpairsFeatures.png}
  \end{center}
\end{minipage}

\begin{minipage}[t]{0.5\textwidth}
  \subsection*{Figure S5}
  \R{} code for this figure is documented in Section \ref{screenplot}.
  \begin{center}
    \vspace{15ex}
    \includegraphics[width=1.0\textwidth]{result/Figures/screenPlot.pdf}
  \end{center}
\end{minipage}
\begin{minipage}[t]{0.5\textwidth}
  \subsection*{Figure S6}
  \R{} code for this figure is documented in Section \ref{distributionOfInteractions}.
  \begin{center}
    \includegraphics[width=1.0\textwidth]{result/Figures/distributionOfInteractions.pdf}
  \end{center}
\end{minipage}

\par\endgroup