Commit 5b5c03c3 authored by Jerome Mariette's avatar Jerome Mariette

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......@@ -49,6 +49,8 @@
%%% Load packages
\usepackage{listings}
\usepackage{color}
\usepackage{lineno}
\linenumbers
\definecolor{gray}{rgb}{0.5,0.5,0.5}
\lstset{
language=Java,
......@@ -287,11 +289,11 @@ http://bioinfo.genotoul.fr/jvenn.
High-throughput biology has led to an increasing number of data, with more and
more complex experimental designs. The analysis of these data often produces
biological identifier lists, including gene names or operational
taxonomic units, obtained from different methods (for differential analysis)
or from different experimental conditions. Venn diagrams \cite{Venn1880} are a
common visualization chart, which allows to spot shared and unshared identifiers
providing an insight on lists similarities.
biological identifier lists, including gene names or OTU (Operational Taxonomic
Unit), obtained from different methods (for differential analysis) or from
different experimental conditions. Venn diagrams \cite{Venn1880} are a common
visualization chart, which allows to spot shared and unshared identifiers
providing an insight on lists similarities.
In a Venn diagram, each list is presented by a transparent shape. Shape overlaps
contain the elements shared between lists or more often the corresponding counts.
......@@ -304,16 +306,18 @@ representation introduces new shapes providing a clearer view, shown in the
example of Fig.~\ref{fig::edwards}.
Many Venn diagram software packages are already available. The first six lines
of Table~\ref{table::features} present a subset of selected packages with their
of Table~\ref{table::features} present the main packages with their
main features (maximum number of input lists, input data formats, Venn diagram
layouts, application types and output formats). The table gives insight on
several aspects of Venn diagram production and highlights that, up to now, no
web application handled up to six lists. VENNTURE \cite{Bronwen2012} is the only
application able to produce such diagrams but it only implements Edwards layout
and runs only under MS-Windows OS, producing static MS-PowerPoint and MS-Excel
files. Proportional Venn diagrams can only display a very limited number of lists,
three at maximum. Therefore, as jvenn was designed to display up to six lists,
this one, does not implement proportional diagrams.
several aspects of the Venn diagram production and highlights that, up to now,
no web application handled up to six lists. VENNTURE \cite{Bronwen2012} is the
only application able to produce such diagrams but it only implements Edwards
layout and runs only under MS-Windows OS, producing static MS-PowerPoint and
MS-Excel files. Proportional Venn diagrams can only display a very limited
number of lists, three at maximum. The only feature available in other software
which is not in jvenn is the proportional diagram. This is justified by the fact
that jvenn was designed to display up to six lists and that proportional diagram
is not suited to visualize more than three lists.
Hereafter we introduce jvenn, a JavaScript library, developed as a jQuery
plug-in \cite{jquery}, including many features easing diagram production and
......@@ -343,10 +347,10 @@ Table~\ref{table::format}, where the different lists are ``sample1'' and
Finally, ``Count lists'' provide a count number for each element of a list.
Hence, with ``Count lists'' the figures presented in the diagram correspond to
the sums of counts of all elements shared between lists. they can be
particularly useful to present OTU (Operational Taxonomic Unit) read counts. For
particularly useful to present OTU read counts \cite{Aravindraja2013}. For
``Lists'' and ``Count lists'', jvenn computes the intersection counts and
displays the chart. For ``intersection counts'', the intersection counts is
provided by the user.
provided by the user.
\subsection*{Display features}
......@@ -437,29 +441,52 @@ file with all the intersection contents.
\section*{Discussion}
Fig.~\ref{fig::edwards}, outputed by jvenn, presents all the lists overlaps. The
highest values are located in central areas of the graph, showing that the corresponding methods
share large portions of gene lists. Finally, taking advantage of jvenn's panel
button, a list of 484 genes shared by DESeq, TMM, UQ and FQ has been extracted.
One of the 5,277 genes was randomly choosen (G002562) and sought using jvenn
search box. It was found to be part of the five genes shared by FQ and UQ.
The lists overlaps, as produced by jvenn, are given in Fig.~\ref{fig::edwards}
(Edwards layout) and \ref{fig::features} (standard layout). The highest counts
are located in central areas of the graph, showing that the corresponding
methods share large portions of gene lists. The jvenn statistics show that the
different methods produce gene lists with very different sizes (minimum 417 -
maximum 1,249) and that most of the genes are shared between methods: 1,069
genes out of 1,347 are common between at least four methods.
In a very intuitive manner, the chart also points out that the results are
strongly consensual since there are many zeros in the peripheral areas. Only a
few genes (114) are specific to one list only (24 for FQ, 27 for UQ and 63 for
DESeq, which appears to be the less restrictive method, as shown in the barplot
below the Venn diagram, and also the most different from the others).
Genes that are in two lists only are also very few (47: 13 for DESeq and TMM, 5
for UQ and FQ, 15 for TMM and UQ, 8 for FQ and DESeq and 6 for DESeq and UQ).
Note that all these numbers are easily read from the chart and that the strong
consensus between the lists is also clearly shown from the upper side figure
``Number of elements: specific or shared by several lists''). Such findings are
not easily shown using only contingency tables.
The largest count over all lists overlaps is found to be 484, which is the
number of genes found to be differential by DESeq, TMM, UQ and FQ. As shown in
Fig~\ref{fig::web}, this list is very easily retrieved from the web application
in one click only, providing the biologist with a large list of very consensual
list to study.
On the other hand, if the biologist is interested in one specific gene, this
gene can easily be tracked using the search box at the top side of
Fig.~\ref{fig::web}. As no specific gene is of interest in the seminal work, we
simply picked out one of the 5,277 genes randomly (G002562) and used it in the
search box. It was found to be part of the five genes specific to FQ and UQ.
Making the same analysis with VENNTURE is also possible but a bit harder: the
484 genes shared by DESeq, TMM, UQ and FQ can be found easily in the
intersection spreadsheet outputed by VENNTURE but the diagram did not allow
to search for gene G002562. Thus, this gene has to be found using MS-Excel text
search in the intersection spreadsheet, which is less handy than a dynamic and
interactive search. Moreover, the additional statistics are not provided by the
tool.
In the same way, the 484 genes shared by DESeq, TMM, UQ and FQ were found
in the intersection spreadsheet outputed by VENNTURE. The diagram did not allow
to search for gene G002562, which was was found using MS-Excel text search in
the intersection spreadsheet nevertheless.
The jvenn statistics show that the different methods produce gene lists with
very different sizes (minimum 417 - maximum 1,249) and that most of the genes are
shared between methods: 1,069 genes out of 1,347 are common between at least
four methods.
\section*{Conclusion}
jvenn enables to compare up to six lists and updates the diagram automatically
when modifying the lists content. Compared to VENNTURE it does not need any
local installation of a new program and it gives access to a dynamic diagram
providing simple functions to extract gene lists and perform searches.
providing simple tools to extract gene lists and perform searches.
jvenn's statistics charts give a simple and quick overview of the sizes of the
different lists and of their overlaps. It permits to compare different Venn
diagrams. These features are not available in the VENNTURE software package.
......@@ -471,14 +498,14 @@ genes, these features ease the analysis.
Thanks to its numerous features, dynamic behavior and graphical layout quality,
jvenn can be efficiently used in many cases to compare different sets of results
and easily extract shared elements. Being a simple JavaScript plug-in allows to
embed it in any web environment.
and easily extract shared elements. Being a simple JavaScript plug-in allows
developers to embed it in any web environment.
\section*{Availability and requirements}
jvenn is freely available under the GNU General Public License (GPL) and can be
downloaded with an example and the full documentation at
downloaded with an example and its full documentation at
http://bioinfo.genotoul.fr/jvenn website. A running version is accessible at
http://bioinfo.genotoul.fr/jvenn/example.html.
......
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