Commit 3dd7b174 authored by Jerome Mariette's avatar Jerome Mariette

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......@@ -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.},
......
......@@ -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}
......
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