Commit 472ae2cf authored by waldispuhl's avatar waldispuhl
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format supp mat

parent 8cf26052
......@@ -110,6 +110,8 @@ The following molecules were not integrated in our benchmark because they are ar
\textbf{Answer:} \textit{We updated the Figure as suggested and added arrows to mark the positions. Unfortunately, we did not managed to produce a clearer picture using a cutaway view. Nonetheless, we believe that the arrows already improve the clarity of the figure.}\\
Finally, in this revision we also removed Figures 4 (illustration of a disruption profile) and~6 (example of a ROC curve) from the previous manuscript as we do not think they bring much information, neither help to clarify the message of this work.\\
Overall, we would like to thank the reviewer for his careful reviews and helpful comments.
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......@@ -104,11 +104,30 @@
\newcommand{\rnasnp}{\texttt{RNAsnp}\xspace}
%% for last Table
\usepackage{array}
\newcolumntype{L}[1]{>{\raggedright\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}
\newcolumntype{C}[1]{>{\centering\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}
\newcolumntype{R}[1]{>{\raggedleft\let\newline\\\arraybackslash\hspace{0pt}}m{#1}}
\usepackage{diagbox}
\newcommand*\mc[1]{\multicolumn{1}{c}{#1}}
\newcommand{\raisehdr}[1][.5\normalbaselineskip]{\raisebox{#1}}
% Title
\title{Supplementary Material for ``Combining structure probing data on RNA mutants with evolutionary information reveals RNA-binding interfaces''}
\author{Vladimir Reinharz$^1$, Yann Ponty$^2$, J\'er\^{o}me Waldisp\"{u}hl$^1$}
\date{\small $^1$ School of Computer Science, McGill University, Montreal, Canada\\$^2$ Laboratoire d'informatique, \'Ecole Polytechnique, Palaiseau, France.}
\begin{document}
\section{Supplementary data}
\subsection{Alternative Measures}
\maketitle
\section*{Alternative Measures}
The results when different measures are used to evaluate the \shape profile distances.
......@@ -142,8 +161,7 @@ The second is a variant which considers the maximally contributing window over t
\end{figure}
\subsection{\remu and \shape intersection}
\section*{\remu and \shape intersection}
Given the mutation ranked by structural disruption by \shape experiments and \remu. At every percentile, we look at the
intersection between the elements in those set over their respective percentile. In Fig.~\ref{fig:percentile} we show on the $y$ axis the percentiles and on the $x$ the ratio of those sizes over the maximal number possible.
\begin{figure}[ht!]
......@@ -163,7 +181,7 @@ We then evaluated the AUCs using for every cutoff percentile $\delta$ the mutati
\label{fig:remushape}
\end{figure}
\subsection{Rfam matches and remuRNA}
\section*{Rfam matches and remuRNA}
Evaluations of AUCs on every sequence in the PDB database matching a Rfam family with a length smaller than 150 nucleotides is shown in Fig.~\ref{fig:all_rfam_auc}. The 14 families
are:
\begin{itemize}
......@@ -191,7 +209,7 @@ are:
\label{fig:all_rfam_auc}
\end{figure}
\subsection{glycine riboswitch}
\section*{glycine riboswitch}
Results for the glycine riboswitch with the 4 different distance MaM experiments is shown in Fig.~\ref{fig:glyc_dist_4}.
\begin{figure}[ht!]
\centering
......@@ -200,64 +218,68 @@ Results for the glycine riboswitch with the 4 different distance MaM experiments
\label{fig:glyc_dist_4}
\end{figure}
\subsection{c-di-GMP pocket}
\section*{c-di-GMP pocket}
The results for c-di-GMP having as positive positions the ones interacting in the binding pocket and with or without the interaction with the other molecules in the PDB is shown in Fig.~\ref{fig:cdigmp_hairpinornot}
\begin{figure}[ht!]
\centering
\begin{subfigure}[b]{0.45\textwidth}
\includegraphics[width=1.4\textwidth]{FigureS8}
\begin{subfigure}[b]{0.4\textwidth}
\includegraphics[width=1\textwidth]{FigureS8}
\caption{MaM}
\end{subfigure}
\begin{subfigure}[b]{0.45\textwidth}
\includegraphics[width=1.4\textwidth]{FigureS8b}
\begin{subfigure}[b]{0.4\textwidth}
\includegraphics[width=1\textwidth]{FigureS8b}
\caption{remuRNA}
\end{subfigure}
\caption{On the first row the AUC values given the pocket and the protein, while on the second row we only consider the pocket as positive values.}
\label{fig:cdigmp_hairpinornot}
\end{figure}
\subsection{adenine MaM without ligand}
\newpage
\section*{adenine MaM without ligand}
We show in Fig.~\ref{fig:adenine_4} the results for the adenine riboswitch when the disruption is based on a MaM experiment in absence of the adenine ligand.
\begin{figure}[ht!]
\centering
\includegraphics[width=\textwidth]{FigureS9}
\includegraphics[width=0.4\textwidth]{FigureS9}
\caption{AUC results for the adenine riboswitch when the disruption is based on a MaM experiment in absence of the ligand}
\label{fig:adenine_4}
\end{figure}
\subsection{tRNA positions extrapolated from PDB \texttt{3J78}}
\section*{tRNA positions extrapolated from PDB \texttt{3J78}}
We show in Fig.~\ref{fig:trna} the results for the tRNA when binding interfaces are extrapolated form PDB \texttt{3J78}.
\begin{figure}[ht!]
\centering
\includegraphics[width=\textwidth]{FigureS10}
\includegraphics[width=0.4\textwidth]{FigureS10}
\caption{AUC results for the tRNA when the binding interfaces are extrapolated form PDB \texttt{3J78}}
\label{fig:trna}
\end{figure}
\vspace{0em}
\newpage
\section{Dataset binding positions}
\section*{Dataset of binding positions}
\begin{table}[ht!]
\rotatebox{90}{
\begin{tabular}{lllll}
%\rotatebox{90}{
\scalebox{0.8}{
\begin{tabular}{llllL{6cm}}
RNA & Binding to & RFAM & PDB(s) &Binding Positions on PDB \\\hline\hline
5S & Prots. & RF00001 & 2WWQ & $7-13,27-33,38,41-57,59-60,70,73-84,88-104,112-116$\\
& & & 3OAS & $6-12,26-33,37-38,41-52,54-57,59,70,73-84,88-104,112-116$\\
& & & 3OFC & $6-12,27-31,33,37-38,41-52,54-59,73-84,88-104,112-117$\\
& & & 3ORB & $6-12,27-31,33,37-38,41-52,54-59,73-84,88-104,112-116$\\\hline
5S & \raisehdr{Prots.} & \raisehdr{RF00001} & \raisehdr{2WWQ} & $7-13,27-33,38,41-57,59-60,70,73-84,88-104,112-116$\\
& & & \raisehdr{3OAS} & $6-12,26-33,37-38,41-52,54-57,59,70,73-84,88-104,112-116$\\
& & & \raisehdr{3OFC} & $6-12,27-31,33,37-38,41-52,54-59,73-84,88-104,112-117$\\
& & & \raisehdr{3ORB} & $6-12,27-31,33,37-38,41-52,54-59,73-84,88-104,112-116$\\\hline
tRNA & anticodon & RF00005 & & $34-36$\\
& T-$psi$-C-G & & & $54-57$\\
& Prot. DNA & & 1EHZ & 1, 19, $34-36$, $56- 57$, $73-76$\\ \hline
c-di-GMP ribo. & c-di-GMP & RF01051 & c-di-GMP pocket & $11-13, 40-41, 83$\\\hline
cobalamin ribo. & B1Z & RF00174 & 4GXY & $41-43,64-66,72-78,106,108-109,124,148-150,155-157,159-162$\\\hline
cobalamin ribo. & \raisehdr{B1Z} & \raisehdr{RF00174} & \raisehdr{4GXY} & $41-43,64-66,72-78,106,108-109,124,148-150,155-157,159-162$\\\hline
adenine ribo. & adenine & RF00167 & 1Y26 & $21-22,47,50-52,73-75$\\\hline
glycine ribo. & glycine & RF00504 & 3P49 & $35-39, 46, 48-42, 110-114,137, 139-143$\\
glycine ribo. & \raisehdr{glycine} & \raisehdr{RF00504} & \raisehdr{3P49} & $35-39, 46, 48-42, 110-114,137, 139-143$\\
\end{tabular}
}
\caption{For each RNA some info}
\caption{Binding positions for the mutate-and-map dataset. This table also provide the reference PDB structure and Rfam family used in our benchmark.}
\label{table:datasetinfo}
\end{table}
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