Commit 098df5d5 authored by Türei Dénes's avatar Türei Dénes

files instead of symlinks :)

parent d25d04a4
../Dokumentumok/pw/slides/beamer_embl.tex
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% EMBL(-EBI) style template for XeLaTeX Beamer
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% Copyright (c) 2014-2015 - EMBL-EBI
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% File author(s): Dénes Türei (denes@ebi.ac.uk)
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% Distributed under the GPLv3 License.
% See accompanying file LICENSE or a copy at
% http://www.gnu.org/licenses/gpl-3.0.html
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% Website: http://www.ebi.ac.uk/~denes
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% This template has been made according to the
% EMBL style guidelines.
% Please see the URLs below for more details.
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% http://intranet.ebi.ac.uk/sites/intranet.ebi.ac.uk/files/content/outreach/EMBL_branding_guidelines.pdf
% http://intranet.ebi.ac.uk/outreach/writing-embl-style-guide
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% Tested with XeTeX, Version 3.14159265-2.6-0.99991
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\documentclass[aspectratio=1610]{beamer} % this is for 16:10 wide screens
% set this according to the actual presentation room
% XeLaTeX packages
\usepackage[no-math]{fontspec}
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\usepackage{xltxtra}
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% we don't need all of these all the time
\usepackage{graphicx}
\usepackage{tikz}
\usepackage{xcolor,color}
\usepackage{booktabs}
\usepackage{hyperref}
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% Figure numbering
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% here you can put anything what will appear in the left top corner green square:
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% here you set short title, full title, your name(s), institute, and other affiliations, and the date
\title[Literature curated pathways]{Pathways: causality and mechanisms behind patterns. Resources, methods, applications}
\author{Denes Turei}
\institute{\begin{tiny}Saez-Rodriguez group (EMBL Hinxton)\par Overington group (EMBL Hinxton)\par Gavin group (EMBL Heidelberg)\par\end{tiny}\vspace*{\baselineskip} EMBL-EBI\hspace*{0.247em}\raisebox{-1.21ex}{\includegraphics[height=3.80ex]{embl1.pdf}} }
\date{4th June 2015}
% or if you compile the document on the day of your presentation:
% \date{\today}
% optionally, your email:
%\\{\footnotesize turei.denes@gmail.com}
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\begin{document} %
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\newcounter{thepic} \setcounter{thepic}{1}
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\frame{\titlepage \vspace{-0.5cm}}
% new section
\section{Intro}
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% sample slides (titles, subtitles, itemize, placement with tikz, etc.) %
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\begin{frame}{Signaling networks and pathways}
\begin{tikzpicture}
\node[anchor=north west] at (0.6,0) {
\begin{minipage}{0.75\textwidth}
{\color{emblgreen} Interactomes vs. pathways}\\
\begin{itemize}
\item PPI network: binary interactions
\item Pathways: directions, signs $=$ causality
\item High vs. low throughput experiments
\item Literature curation
\end{itemize}
\vspace*{0.66\baselineskip}
High quality $\Longleftrightarrow$ high coverage\vspace*{0.33\baselineskip}\\
{\color{emblgreen} Criticism}\\
\begin{itemize}
\item Curation mistakes
\item Research bias
\end{itemize}
\end{minipage}};
\node[anchor=north east] at (0,0) {\includegraphics[width=0.33\textwidth]{pathway.pdf}};
\end{tikzpicture}
\end{frame}
\begin{frame}{Objectives}
{\color{emblgreen}\Large Signalling network}
\begin{itemize}
\item High quality pathways
\item Manually curated, from low-throughput studies
\item Directed and signed edges where it's possible
\item Structural and functional annotations
\end{itemize}
{\color{emblgreen}\Large Software}
\begin{itemize}
\item Python modules
\end{itemize}
{\color{emblgreen}\Large Possible applications}
\begin{itemize}
\item Modeling
\item Graph topology and dynamics
\end{itemize}
\end{frame}
\begin{frame}{}
\begin{center}
%\includegraphics[width=0.4\textwidth]{kirouac_hmap.png}
\end{center}
\begin{flushright}
Edge consistency \textbullet\ from Kirouac et al. 2012
\end{flushright}
\end{frame}
\section{Pathways}
\begin{frame}{Resources: content}
\vspace*{-1ex}
%\includegraphics[width=\textwidth]{../a2/src/results/databases-clpce.pdf}
\end{frame}
\begin{frame}{Pathway resources}
\begin{block}{Resources (27)}
{\color{emblgreen} Directed} (13)\\
ARN, CA1, DEPOD, DOMINO, Guide2Pharmacology, HPRD, Macrophage, NCI-PID, NRF2ome, PDZBase, PhosphoSite, SPIKE, SignaLink2, Signor, dbPTM, phosphoELM\\
{\color{emblgreen} Non-directed} (11)\\
AlzPathway, CancerCellMap, DIP, DOMINO, DeathDomain, ELM, InnateDB, IntAct, MPPI, MatrixDB, NetPath\\
\end{block}
\begin{itemize}
\item Size (giant component): 7,088 nodes, 35,147 edges
\item 21,294 PubMed IDs
\item 20,738 directed edges
\item Diameter: 12, mean degree: 9.74
\item Directions, signs
\item Various annotations (localization, role, etc)
\end{itemize}
\end{frame}
\begin{frame}{Coverage}
{\color{emblgreen}\textasciitilde30$\,$\% of the human proteome}\par
{\color{emblred}\textasciitilde80$\,$\% of the cancer dirvers and drug targets}\par
{\color{emblyellow}\textasciitilde20$\,$\% of proteins have known compounds}\par
{\color{emblgray75}\textasciitilde90$\,$\% of proteins are in proteomics datasets}\par
\end{frame}
\section{Alternatives}
\begin{frame}{Alternatives: PathwayCommons, ConsensusPathDB}
{\color{emblgreen}\Large PathwayCommons} \hfill {\color{emblpetrol}\footnotesize\textbullet\ http://pathwaycommons.org/}
\begin{itemize}
\item 18 resources {\footnotesize – only IntAct in common with my network}
\item Vast amount of HTP data
\item References and evidences only in BioPax format
\item R package: Paxtools
\end{itemize}
{\color{emblgreen}\Large ConsensusPathDB} \hfill {\color{emblpetrol}\footnotesize\textbullet\ http://consensuspathdb.org/}
\begin{itemize}
\item 15 resources {\footnotesize – 6 also in my network}
\item Not only direct physical and biochemical interactions
\item Clear references
\item Web based gene set analysis
\end{itemize}
\end{frame}
\section{}
\begin{frame}{Acknowledgements}
{\color{emblgreen}\Large Systems Biomedicine Group, EMBL-EBI, Hinxton}\\
\begin{itemize}
\item Julio Saez-Rodriguez\\
\item {\footnotesize Luz Garcia Alonso, Thomas Cokelaer, Lekshmi Dharmarajan, Federica Eduati, Marti Bernardo Faura, Emanuel Gonçalves,Francesco Iorio, Angeliki Kalamara, Victoria Doldan Martelli, Michael Schubert, Michael Menden}
\end{itemize}
{\color{emblgreen}\Large EIPOD fellowship}\\
\begin{itemize}
\item John Overington (ChEMBL Group, EMBL-EBI, Hinxton)
\item Anne-Claude Gavin (Biomolecular Networks Group, EMBL Heidelberg)
\end{itemize}
Tamas Korcsmaros (TGAC \& IFR, Norwich)\\
NetBiol Group, Eotvos University, Budapest, Hungary\\
Link Group, Semmelweis University, Budapest, Hungary\\
\end{frame}
\end{document}
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../Dokumentumok/pw/a2/src/bioigraph/data/embl_colors
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0.431373, 0.662745, 0.270588, Mantis
0.517647, 0.705882, 0.360784, Feijoa
0.592157, 0.745098, 0.45098, Chelsea cucumber
0.662745, 0.788235, 0.545098, Madang
0.803922, 0.87451, 0.733333, Pale leaf
0.87451, 0.917647, 0.823529, Willow brook
0.937255, 0.956863, 0.913725, Twilight blue
0, 0.482353, 0.498039, Teal
0, 0.533333, 0.545098, Dark cyan
0.286275, 0.588235, 0.603922, Blue chill
0.435294, 0.65098, 0.662745, Neptune
0.678431, 0.784314, 0.788235, Jungle mist
0.792157, 0.854902, 0.858824, Zumthor
0.894118, 0.92549, 0.92549, Zircon
0.988235, 0.8, 0.0235294, Gold
0.992157, 0.819608, 0.133333, Turbo
0.992157, 0.843137, 0.247059, Golden dream
0.992157, 0.866667, 0.364706, Kournikova
0.996078, 0.917647, 0.611765, Vis vis
1, 0.945098, 0.737255, Mint julep
1, 0.972549, 0.866667, Cornsilk
0.854902, 0, 0.145098, Crimson
0.870588, 0.231373, 0.203922, Tomato
0.886275, 0.360784, 0.286275, Flamingo
0.909804, 0.478431, 0.384314, Flame pea
0.94902, 0.701961, 0.619608, Wax flower
0.968627, 0.807843, 0.745098, Watusi
0.984314, 0.901961, 0.870588, Bridesmaid
0, 0, 0, Black
0.270588, 0.266667, 0.278431, Bastille
0.392157, 0.396078, 0.403922, Dim gray
0.505882, 0.509804, 0.517647, Aluminium
0.713726, 0.717647, 0.72549, Gray
0.811765, 0.815686, 0.819608, Iron
0.905882, 0.909804, 0.913725, Athens grey
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