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BMC_jvenn/bmc_jvenn.bib

@@ -31,6 +31,13 @@
   pages = {61–76}
 }
 
+@ARTICLE{Dillies2012,
+  author = {Marie-Agnès Dillies, Andrea Rau, Julie Aubert, Christelle Hennequet-Antier, Marine Jeanmougin, Nicolas Servant, Céline Keime, Guillemette Marot, David Castel, Jordi Estelle, Gregory Guernec, Bernd Jagla, Luc Jouneau, Denis Laloë, Caroline Le Gall, Brigitte Schaëffer, Stéphane Le Crom, Mickaël Guedj and Florence Jaffrézic, on behalf of The French StatOmique Consortium},
+  title = {A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis.},
+  journal = {Briefings in Bioinformatics},
+  year = {2012}
+}
+
 @ARTICLE{DeuPons2014,
   author = {Jordi Deu-Pons and Michael P Schroeder and Nuria Lopez-Bigas},
   title = {jHeatmap: an interactive heatmap viewer for the web.},

BMC_jvenn/bmc_jvenn.tex

@@ -204,7 +204,10 @@
 
 \begin{abstract} % abstract
 \parttitle{Background} %if any
-Venn diagrams are commonly used to present list comparison results. When the number
+Venn diagrams are commonly used to present list comparison results. For example, 
+biologists show differences between gene lists originating from different 
+conditions this way. It is also a standard tool to display method comparison results 
+in bioinformatics. When the number
 of input lists exceeds four the diagram becomes difficult to read. Alternative layouts
 and dynamic display features can improve its readability.
 
@@ -281,14 +284,19 @@ http://bioinfo.genotoul.fr/jvenn.
 
 \section*{Background}
 
-List comparison results are often presented as Venn diagrams \cite{Venn1880}. In
-a Venn diagram each list is figured by a transparent shape. Shape overlaps
+With the advent of high-throughput biology the number of compared samples, within an experiment, is increasing.
+The analysis step often leads to the production of a biological 
+identifier list, such as gene names or operational taxonomic units, for each sample.
+A common visualization chart is the Venn diagrams \cite{Venn1880} which allows to spot 
+shared and unshared identifiers providing an insight on the similarities between the lists.
+
+In a Venn diagram each list is figured by a transparent shape. Shape overlaps
 contain the elements shared between lists or more often the corresponding counts.
 In proportional Venn diagrams the size of a shape depends on the number of
 elements of the corresponding list intersection. Venn diagram with up to four 
 lists are easy to read and understand, but they become difficult to interpret
 with more lists. To solve this problem, the Edwards-Venn \cite{Edwards2004}
-representation introduces new shapes providing a clearer view (Fig. 2).
+representation introduces new shapes providing a clearer view.
 
 Many Venn diagram software packages are already available. The first six lines
 of Table 1 present a subset of selected packages with their features including 
@@ -334,7 +342,7 @@ representation. But then, the intersection areas are often too small to display
 the figures.
 
 To present, in a user-friendly manner, five or six list diagrams, jvenn implements
-(Fig. 1) several functionalities. First, the display can be switched to Edwards-Venn
+several functionalities. First, the display can be switched to Edwards-Venn
 (Fig. 2) which gives a clearer graphical representation for six list diagrams. To
 enhance the figure's readability on the classical six lists Venn graphic, it was
 decided not to present all the values and to link some areas to their figures
@@ -352,8 +360,8 @@ homogeneity of the input list sizes. The intersection size graph can be used to
 compare the compactness of multiple Venn diagrams.
 
 For more than three lists diagrams, jvenn presents a switch button panel to 
-highlight intersections (Fig. 1). It also provides two extra charts (Fig. 1) 
-located bellow the Venn. The first one represents the input lists size
+highlight intersections (Fig. 1). It also provides two extra charts (Fig. 1 and
+Fig. 2) located bellow the Venn. The first one represents the input lists size
 histogram. The second one displays the number of elements in intersections of a
 certain size. It includes, as well, search and intersection identifiers export 
 functions.
@@ -380,25 +388,36 @@ available as a Web application at http://bioinfo.genotoul.fr/jvenn/example.html
 The installation documentation is included in the software package which can be
 downloaded from http://bioinfo.genotoul.fr/jvenn.
 
+\subsection*{Performances}
+
+jvenn's performance depends on the client browser. Using the running version
+on a standard Linux computer (one cpu, 4GB of RAM), it displays a six lists
+diagram of 10 000 identifiers in two seconds.
+
 
 \section*{Results}
 
-First, considering \textit{Bos torus}, \textit{Gallus gallus}, \textit{Homo
-sapiens}, \textit{M. domestic}, \textit{M. mulatta} and \textit{Mus musculus}
-the 6 species with the largest number of annotations in miRBase
-\cite{Kozomara2013}. All micro RNAs for each species have been extracted and
-imported using jvenn. The resulting chart presented on Fig. 3 highlights xx
-miRNAs shared between.
+M.A. Dillies and colleagues \cite{Dillies2012} have compared seven RNA-Seq data
+normalization methods and given a set of best practices to help biologists in their data processing. In table two, they 
+have shown the differences between methods pair-wise. 
+The raw data table provided by the team contains 5,277 lines and eight columns. The columns correspond to
+the different methods presented in the 'Differential expression analysis' section of the article. The data in the  
+table was thresholded ($p < 0.05$) to produce the method specific gene name lists. Six out of seven methods were
+selected for further processing ; Med was left out. The list were uploaded to the jvenn application and a 
+Venn diagram was produced. 
 
+In the discussion section of the article the author 
 
+The jvenn statistics show that the different methods produce gene lists with very different sizes (minimum
+417 - maximum 1,249) and the most of the genes are shared between methods : 1,069 genes out of 1,347 shared 
+by at least four methods.
 
 
-jvenn's performance depends on the client browser. Using the running version
-on a standard Linux computer (1 cpu, 4GB of RAM), it displays a six lists
-diagram of 10 000 identifiers in two seconds.
 
 \section*{Discussion}
 
+Even if this kind of comparison gives some insight on the method result overlap.
+
 
 \section*{Conclusions}