bmc_jvenn.tex 30.3 KB
 Jerome Mariette committed Mar 03, 2014 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 %% BioMed_Central_Tex_Template_v1.06 %% % % bmc_article.tex ver: 1.06 % % % %%IMPORTANT: do not delete the first line of this template %%It must be present to enable the BMC Submission system to %%recognise this template!! %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% LaTeX template for BioMed Central %% %% journal article submissions %% %% %% %% <8 June 2012> %% %% %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% For instructions on how to fill out this Tex template %% %% document please refer to Readme.html and the instructions for %% %% authors page on the biomed central website %% %% http://www.biomedcentral.com/info/authors/ %% %% %% %% Please do not use \input{...} to include other tex files. %% %% Submit your LaTeX manuscript as one .tex document. %% %% %% %% All additional figures and files should be attached %% %% separately and not embedded in the \TeX\ document itself. %% %% %% %% BioMed Central currently use the MikTex distribution of %% %% TeX for Windows) of TeX and LaTeX. This is available from %% %% http://www.miktex.org %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%% additional documentclass options: % [doublespacing] % [linenumbers] - put the line numbers on margins %%% loading packages, author definitions %\documentclass[twocolumn]{bmcart}% uncomment this for twocolumn layout and comment line below \documentclass{bmcart} %%% Load packages  Jerome Mariette committed Mar 20, 2014 50 51 52 53 54 55 56 57 58 59 60 61 62 \usepackage{listings} \usepackage{color} \definecolor{gray}{rgb}{0.5,0.5,0.5} \lstset{ language=Java, showstringspaces=false, columns=flexible, basicstyle={\scriptsize \ttfamily}, numbers=none, stringstyle=\color{gray}, breaklines=true, breakatwhitespace=true }  Jerome Mariette committed Mar 03, 2014 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 %\usepackage{amsthm,amsmath} %\RequirePackage{natbib} %\RequirePackage{hyperref} \usepackage[utf8]{inputenc} %unicode support %\usepackage[applemac]{inputenc} %applemac support if unicode package fails %\usepackage[latin1]{inputenc} %UNIX support if unicode package fails %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% If you wish to display your graphics for %% %% your own use using includegraphic or %% %% includegraphics, then comment out the %% %% following two lines of code. %% %% NB: These line *must* be included when %% %% submitting to BMC. %% %% All figure files must be submitted as %% %% separate graphics through the BMC %% %% submission process, not included in the %% %% submitted article. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \def\includegraphic{} \def\includegraphics{} %%% Put your definitions there: \startlocaldefs \endlocaldefs %%% Begin ...  Jerome Mariette committed Aug 05, 2014 98 \begin{document}\sloppy  Jerome Mariette committed Mar 03, 2014 99 100 101 102 103  %%% Start of article front matter \begin{frontmatter} \begin{fmbox}  Jerome Mariette committed May 06, 2014 104 \dochead{Software}  Jerome Mariette committed Mar 03, 2014 105 106 107 108 109 110 111  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter the title of your article here %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  Jerome Mariette committed May 05, 2014 112 \title{jvenn: an interactive Venn diagram viewer.}  Jerome Mariette committed Mar 03, 2014 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter the authors here %% %% %% %% Specify information, if available, %% %% in the form: %% %% ={,} %% %% = %% %% Comment or delete the keys which are %% %% not used. Repeat \author command as much %% %% as required. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \author[  Jerome Mariette committed Mar 11, 2014 129 130 131 132 133 134  addressref={aff2}, % id's of addresses, e.g. {aff1,aff2} noteref={n1}, % id's of article notes, if any email={Philippe.Bardou@toulouse.inra.fr} % email address ]{\inits{PB}\fnm{Philippe} \snm{Bardou}} \author[ addressref={aff1},  Jerome Mariette committed Mar 03, 2014 135 136  corref={aff1}, % id of corresponding address, if any noteref={n1}, % id's of article notes, if any  Jerome Mariette committed Mar 11, 2014 137 138  email={Jerome.Mariette@toulouse.inra.fr} ]{\inits{JM}\fnm{J\'{e}r\^{o}me} \snm{Mariette}}  Jerome Mariette committed May 22, 2014 139 140 141 \author[ addressref={aff1}, email={Frederic.Escudie@toulouse.inra.fr}  Jerome Mariette committed Jun 02, 2014 142 ]{\inits{FE}\fnm{Fr\'{e}d\'{e}ric} \snm{Escudi\'{e}}}  Jerome Mariette committed Mar 11, 2014 143 144 145 146 \author[ addressref={aff1}, email={Christophe.Djemiel@toulouse.inra.fr} ]{\inits{CD}\fnm{Christophe} \snm{Djemiel}}  Jerome Mariette committed Mar 03, 2014 147 148 \author[ addressref={aff1,aff2},  Jerome Mariette committed Mar 11, 2014 149 150  email={Christophe.Klopp@toulouse.inra.fr} ]{\inits{CK}\fnm{Christophe} \snm{Klopp}}  Jerome Mariette committed Mar 03, 2014 151 152 153 154 155 156 157 158 159 160 161  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter the authors' addresses here %% %% %% %% Repeat \address commands as much as %% %% required. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \address[id=aff1]{% % unique id  Jerome Mariette committed Mar 11, 2014 162 163 164 165 166  \orgname{Plate-forme bio-informatique Genotoul / MIA-T, INRA}, % university, etc \street{Borde Rouge}, % \postcode{31326} % post or zip code \city{Castanet-Tolosan}, % city \cny{France} % country  Jerome Mariette committed Mar 03, 2014 167 168 } \address[id=aff2]{%  Jerome Mariette committed Mar 11, 2014 169 170 171 172 173  \orgname{Plate-forme SIGENAE / GenPhySE, INRA}, % university, etc \street{Borde Rouge}, % \postcode{31326} % post or zip code \city{Castanet-Tolosan}, % city \cny{France} % country  Jerome Mariette committed Mar 03, 2014 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 } %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Enter short notes here %% %% %% %% Short notes will be after addresses %% %% on first page. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{artnotes} %\note{Sample of title note} % note to the article \note[id=n1]{Equal contributor} % note, connected to author \end{artnotes} \end{fmbox}% comment this for two column layout %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% The Abstract begins here %% %% %% %% Please refer to the Instructions for %% %% authors on http://www.biomedcentral.com %% %% and include the section headings %% %% accordingly for your article type. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{abstractbox} \begin{abstract} % abstract  Jerome Mariette committed Mar 03, 2014 206 \parttitle{Background} %if any  Jerome Mariette committed Aug 05, 2014 207 208 209 210 211 212 213 Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus allow the comparison between different experimental conditions or between different methods. However, when the number of input lists exceeds four, the diagram becomes difficult to read. Alternative layouts and dynamic display features can improve its use and its readability.  Jerome Mariette committed Mar 04, 2014 214   Jerome Mariette committed Mar 03, 2014 215 \parttitle{Results} %if any  Jerome Mariette committed Jun 11, 2014 216 217 jvenn is a new JavaScript library. It processes lists and produces Venn diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn  Jerome Mariette committed Aug 05, 2014 218 219 layouts. User interactions can be controlled and customized. Finally, jvenn can easily be embeded in a web page, allowing to have dynamic Venn diagrams.  Jerome Mariette committed Mar 07, 2014 220   Jerome Mariette committed Mar 03, 2014 221 \parttitle{Conclusions} %if any  Jerome Mariette committed Aug 05, 2014 222 jvenn is an open source component for web environments helping  Jerome Mariette committed May 12, 2014 223 scientists to analyze their data. The library package, which comes with full  Jerome Mariette committed Jun 11, 2014 224 documentation and an example, is freely available at  Jerome Mariette committed May 06, 2014 225 http://bioinfo.genotoul.fr/jvenn.  Jerome Mariette committed Mar 20, 2014 226   Jerome Mariette committed Mar 03, 2014 227   Jerome Mariette committed Mar 03, 2014 228 229 230 231 232 233 234 235 236 237 238 \end{abstract} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% The keywords begin here %% %% %% %% Put each keyword in separate \kwd{}. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{keyword}  Jerome Mariette committed Mar 11, 2014 239 240 241 \kwd{Venn} \kwd{Edward-Venn} \kwd{vizualisation}  Jerome Mariette committed Mar 03, 2014 242 \kwd{jquery}  Jerome Mariette committed May 05, 2014 243 \kwd{JavaScript}  Jerome Mariette committed Mar 03, 2014 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 \end{keyword} % MSC classifications codes, if any %\begin{keyword}[class=AMS] %\kwd[Primary ]{} %\kwd{} %\kwd[; secondary ]{} %\end{keyword} \end{abstractbox} % %\end{fmbox}% uncomment this for twcolumn layout \end{frontmatter} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% The Main Body begins here %% %% %% %% Please refer to the instructions for %% %% authors on: %% %% http://www.biomedcentral.com/info/authors%% %% and include the section headings %% %% accordingly for your article type. %% %% %% %% See the Results and Discussion section %% %% for details on how to create sub-sections%% %% %% %% use \cite{...} to cite references %% %% \cite{koon} and %% %% \cite{oreg,khar,zvai,xjon,schn,pond} %% %% \nocite{smith,marg,hunn,advi,koha,mouse}%% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%% start of article main body % %%%%%%%%%%%%%%%% %% Background %% %%  Jerome Mariette committed Mar 03, 2014 286 \section*{Background}  Jerome Mariette committed Mar 04, 2014 287   Jerome Mariette committed Aug 05, 2014 288 289 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  Jerome Mariette committed Aug 06, 2014 290 291 292 293 294 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.  Jerome Mariette committed Jul 23, 2014 295   Jerome Mariette committed Aug 05, 2014 296 In a Venn diagram, each list is presented by a transparent shape. Shape overlaps  Jerome Mariette committed Jun 11, 2014 297 contain the elements shared between lists or more often the corresponding counts.  Jerome Mariette committed Aug 05, 2014 298 299 300 301 302 303 304 In proportional Venn diagrams, the size of a shape is proportional to the number of elements of the corresponding list or of the corresponding lists intersection. Venn diagrams with up to four lists are easy to read and understand but Venn diagrams with more than four lists, are much harder to interpret. To solve this problem, the Edwards-Venn \cite{Edwards2004} representation introduces new shapes providing a clearer view, shown in the example of Fig.~\ref{fig::edwards}.  Jerome Mariette committed Jun 11, 2014 305 306  Many Venn diagram software packages are already available. The first six lines  Jerome Mariette committed Aug 06, 2014 307 of Table~\ref{table::features} present the main packages with their  Jerome Mariette committed Aug 05, 2014 308 309 main features (maximum number of input lists, input data formats, Venn diagram layouts, application types and output formats). The table gives insight on  Jerome Mariette committed Aug 06, 2014 310 311 312 313 314 315 316 317 318 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.  Jerome Mariette committed Jun 11, 2014 319 320 321  Hereafter we introduce jvenn, a JavaScript library, developed as a jQuery plug-in \cite{jquery}, including many features easing diagram production and  Jerome Mariette committed Aug 05, 2014 322 323 324 enhancing their readability. In particular, jvenn can handle up to 6 lists, is a dynamic tool and implements both proportional and Edwards layouts. The library has already been used and cited in two scientific publications  Jerome Mariette committed Aug 05, 2014 325 \cite{Bianchia2013, Aravindraja2013}. It is already embedded in different web  Jerome Mariette committed Aug 05, 2014 326 327 applications such as nG6 \cite{Mariette2012}, RNAbrowse \cite{Mariette} and WallProtDB \cite{SanClemente}.  Jerome Mariette committed Mar 03, 2014 328   Jerome Mariette committed Jul 15, 2014 329   Jerome Mariette committed Mar 05, 2014 330 \section*{Implementation}  Jerome Mariette committed Mar 04, 2014 331   Jerome Mariette committed Aug 05, 2014 332 333 334 335 336 This section presents the main features of the jvenn library, including the kind of inputs it accepts, the different types of charts it displays, the types of the outputs and how it can be integrated in websites or directly used on our example web page.  Jerome Mariette committed Jul 15, 2014 337 \subsection*{Inputs}  Jerome Mariette committed Jun 11, 2014 338   Jerome Mariette committed Aug 05, 2014 339 340 341 342 343 344 345 346 347 The jvenn library accepts three different input formats : Lists'', Intersection counts'' and Count lists''. Examples are presented in Table~\ref{table::format}, where the different lists are sample1'' and sample2'', the elements of the different lists are given in the fields data''. For Intersection counts'', the lists are given a label (A'' or B'') which is used to make the correspondence between the list and its count. 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  Jerome Mariette committed Aug 06, 2014 348 particularly useful to present OTU read counts \cite{Aravindraja2013}. For  Jerome Mariette committed Aug 05, 2014 349 350 Lists'' and Count lists'', jvenn computes the intersection counts and displays the chart. For intersection counts'', the intersection counts is  Jerome Mariette committed Aug 06, 2014 351 provided by the user.  Jerome Mariette committed Mar 07, 2014 352   Jerome Mariette committed Jul 15, 2014 353 \subsection*{Display features}  Jerome Mariette committed Mar 27, 2014 354   Jerome Mariette committed Aug 05, 2014 355 356 Venn diagrams are commonly used to present up to six lists but for six lists, the intersection areas obtained when using a proportional layout are  Jerome Mariette committed Aug 05, 2014 357 often too small to display the figures.  Jerome Mariette committed May 12, 2014 358   Jerome Mariette committed Aug 05, 2014 359 To display five or six lists diagrams, in a user-friendly manner, jvenn  Jerome Mariette committed Aug 05, 2014 360 implements several features.  Jerome Mariette committed Aug 05, 2014 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 First, the layout can be switched between the standard layout and the Edwards-Venn layout (Fig.~\ref{fig::edwards}) which gives a clearer graphical representation for six lists diagrams. To enhance the figure's readability for the classical six lists Venn chart, some count values are not shown and some are display outside the chart, using lines to line the count to its corresponding area. However, this is still not enough to show all figures. Therefore, a switch button panel (right side of Fig.~\ref{fig::features}) was added. It enables to switch on and off the different lists and to display the corresponding intersection counts. When the number of characters of the intersection count exceeds the available space to display it, the value is substituted by a question mark. When the mouse is mouved over this question mark, the value pops-up. To emphasize the list involved in an intersection area, jvenn highlights the intersection shapes when mouse is moved over, fading the others out. The extra charts presented under the Venn diagram ease the verification and comparison of multiple lists. The list size graph allows users to check the  Jerome Mariette committed Jun 11, 2014 378 379 380 homogeneity of the input list sizes. The intersection size graph can be used to compare the compactness of multiple Venn diagrams.  Jerome Mariette committed Jul 24, 2014 381 Scientists are usually interested in extracting identifier lists for some  Jerome Mariette committed Aug 05, 2014 382 383 384 385 intersections, therefore, jvenn implements a one-click function which retrieves the names of the corresponding sets and the identifiers. To find an identifier, one can use a dynamic search box. The shapes containing the matching identifiers are highlighted when using this tool.  Jerome Mariette committed Mar 27, 2014 386   Jerome Mariette committed Jul 15, 2014 387 388 \subsection*{Outputs}  Jerome Mariette committed Aug 05, 2014 389 390 391 392 jvenn display is based on a JavaScript canvas object that allows for PNG export. The intersection table can also be downloaded as a CSV file. This file contains a header line with the diagram area labels and, in column, the identifiers of the elements contained in the area.  Jerome Mariette committed Jul 25, 2014 393 394 395  \subsection*{Integration}  Jerome Mariette committed Aug 05, 2014 396 jvenn allows programmers having only moderate JavaScript experiences to embed  Jerome Mariette committed Aug 05, 2014 397 398 399 Venn diagrams in a web page without dependency. It has been designed following the examples of jbrowse \cite{Westesson01032013}, Cytoscape-Web \cite{Lopes2010}, and jHeatmap \cite{DeuPons2014}.  Jerome Mariette committed Jul 25, 2014 400 401 The integration documentation is included in the software package which can be downloaded from http://bioinfo.genotoul.fr/jvenn.  Jerome Mariette committed Jul 15, 2014 402 403 404  \subsection*{Web application}  Jerome Mariette committed Aug 05, 2014 405 jvenn can also be directly used as a web application, which is available at  Jerome Mariette committed Aug 05, 2014 406 http://bioinfo.genotoul.fr/jvenn/example.html (Fig.~\ref{fig::web}).  Jerome Mariette committed Aug 05, 2014 407 jvenn's web application performances depend on the client browser. Using the  Jerome Mariette committed Aug 05, 2014 408 409 current version on a standard Linux computer (one cpu, four GB of RAM), it displays a six lists diagram of 10,000 identifiers in two seconds.  Jerome Mariette committed Jul 23, 2014 410   Jerome Mariette committed Jul 15, 2014 411 412 413  \section*{Results}  Jerome Mariette committed Aug 05, 2014 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 M.A. Dillies and colleagues \cite{Dillies2012} have compared seven methods for normalization and search of differentially expressed genes in RNASeq data. This study is designed to provide a set of best practices to help biologists with their data processing. Table 2 of the cited article is the contingency table of the differentially expressed genes obtained from the seven methods, where counts in the table correspond to the intersection of two lists obtained from two different methods. The raw data table, kindly provided by the team, contains 5,277 lines and seven columns. The columns correspond to the different methods presented in the Differential expression analysis'' section of their article. The data in the table was filtered ($p < 0.05$) to retrieve the gene name lists corresponding to each method. As, jvenn handles only six list at most, six out of the seven lists were selected for further processing: we left out the median normalization method because, for one hand, this method is very similar to several other methods (as shown in the article) and, for the other hand, we believe that median is a poor estimate of the sequencing length, which is the bias that normalization methods try to correct. The lists were uploaded to the jvenn application and a Venn diagram was obtained, using an Edwards layout, which is shown in Fig.~\ref{fig::edwards}.  Jerome Mariette committed Jul 24, 2014 432   Jerome Mariette committed Jul 25, 2014 433 The same analysis was performed with VENNTURE, the only other tool able to  Jerome Mariette committed Jul 25, 2014 434 generate a six list Edwards Venn diagram. First, the software package was  Jerome Mariette committed Aug 05, 2014 435 436 437 438 installed on a computer running under MS-Windows OS. The six gene lists were loaded in an MS-Excel spreadsheet and VENNTURE was run using the spreadsheet as input generating a static MS-PowerPoint file containing the diagram and a MS-Excel file with all the intersection contents.  Jerome Mariette committed Jul 17, 2014 439   Jerome Mariette committed Jul 24, 2014 440 \section*{Discussion}  Jerome Mariette committed Jul 17, 2014 441   Jerome Mariette committed Aug 06, 2014 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 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.  Jerome Mariette committed Aug 05, 2014 480   Jerome Mariette committed Jul 17, 2014 481   Jerome Mariette committed Aug 05, 2014 482 \section*{Conclusion}  Jerome Mariette committed Mar 03, 2014 483   Jerome Mariette committed Aug 05, 2014 484 485 486 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  Jerome Mariette committed Aug 06, 2014 487 providing simple tools to extract gene lists and perform searches.  Jerome Mariette committed Aug 05, 2014 488 489 490 491 492 493 494 495 496 497 498 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. For biologists using different techniques in their experiment or in their statistical analysis, jvenn enables to quickly extract the shared identifiers. When comparing different methods applied to extract differentially expressed 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  Jerome Mariette committed Aug 06, 2014 499 500 and easily extract shared elements. Being a simple JavaScript plug-in allows developers to embed it in any web environment.  Jerome Mariette committed Jul 25, 2014 501   Jerome Mariette committed Mar 07, 2014 502   Jerome Mariette committed Mar 03, 2014 503 \section*{Availability and requirements}  Jerome Mariette committed Mar 03, 2014 504   Jerome Mariette committed May 12, 2014 505 jvenn is freely available under the GNU General Public License (GPL) and can be  Jerome Mariette committed Aug 06, 2014 506 downloaded with an example and its full documentation at  Jerome Mariette committed May 12, 2014 507 508 http://bioinfo.genotoul.fr/jvenn website. A running version is accessible at http://bioinfo.genotoul.fr/jvenn/example.html.  Jerome Mariette committed Mar 07, 2014 509   Jerome Mariette committed Mar 03, 2014 510 511 512 513 514 515 516 517 518 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Backmatter begins here %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% \begin{backmatter} \section*{Competing interests}  Jerome Mariette committed Mar 11, 2014 519 The authors declare that they have no competing interests.  Jerome Mariette committed Mar 03, 2014 520 521  \section*{Author's contributions}  Jerome Mariette committed May 22, 2014 522 JM conceived and designed the project. JM, PB, FE and CD implemented the project.  Jerome Mariette committed May 12, 2014 523 524 CK evaluated software capabilities, and provided feedback on implementation. JM and CK wrote the manuscript. All authors read and approved the final manuscript.  Jerome Mariette committed Mar 03, 2014 525 526  \section*{Acknowledgements}  Jerome Mariette committed Mar 03, 2014 527 We would like to acknowledge all our users for providing us useful feedback on  Jerome Mariette committed May 23, 2014 528 the system and for pointing out features worth developing. We thank the  Jerome Mariette committed Aug 05, 2014 529 530 531 reviewers and Nathalie Villa-Vialaneix for their insightful and constructive comments. We also thank Julie Aubert and the French StatOmique Consortium for providing us the data used in the Results'' section.  Jerome Mariette committed Mar 03, 2014 532   Jerome Mariette committed Mar 03, 2014 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% The Bibliography %% %% %% %% Bmc_mathpys.bst will be used to %% %% create a .BBL file for submission. %% %% After submission of the .TEX file, %% %% you will be prompted to submit your .BBL file. %% %% %% %% %% %% Note that the displayed Bibliography will not %% %% necessarily be rendered by Latex exactly as specified %% %% in the online Instructions for Authors. %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % if your bibliography is in bibtex format, use those commands: \bibliographystyle{bmc-mathphys} % Style BST file  Jerome Mariette committed Mar 05, 2014 550 \bibliography{bmc_jvenn} % Bibliography file (usually '*.bib' )  Jerome Mariette committed Mar 03, 2014 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572  % or include bibliography directly: % \begin{thebibliography} % \bibitem{b1} % \end{thebibliography} %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Figures %% %% %% %% NB: this is for captions and %% %% Titles. All graphics must be %% %% submitted separately and NOT %% %% included in the Tex document %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% Do not use \listoffigures as most will included as separate files \section*{Figures} \begin{figure}[h!]  Jerome Mariette committed Mar 25, 2014 573  \caption{\csentence{A six lists classic Venn diagram.}  Jerome Mariette committed Aug 05, 2014 574 575 576 577 578  On mouse over a figure, the shape corresponding to the lists involved in the intersection are highlighted and the other ones faded out. In this example, the user pointed the intersection between DESeq, FQ, UQ and TMM which contains 484 different genes. }\label{fig::features}  Jerome Mariette committed Aug 05, 2014 579  \end{figure}  Jerome Mariette committed Mar 03, 2014 580   Jerome Mariette committed Aug 05, 2014 581  \begin{figure}[h!]  Jerome Mariette committed Mar 05, 2014 582  \caption{\csentence{A six lists Edwards-Venn diagram.}  Jerome Mariette committed Aug 05, 2014 583 584 585 586 587 588  This Venn diagram displays overlaps between six different biological samples. The icon, located on the top-right, allows users to download the diagram as a PNG file. The middle-right switch button panel allows to activate or dis-activate lists to access a specific intersection count. Charts showing the list size and intersection size repartition located underneath the diagram.}\label{fig::edwards}  Jerome Mariette committed Aug 05, 2014 589 590 591  \end{figure} \begin{figure}[h!]  Jerome Mariette committed Aug 05, 2014 592 593 594 595 596 597 598 599 600 601  \caption{\csentence{jvenn web application.} The running version of jvenn accessible at http://bioinfo.genotoul.fr/jvenn/example.html. This one allows the user to set all jvenn main features. The layout can be changed from classical to Edwards, a search box is accessible, the switch button panel and the exporting button are available and the statistical charts are displayed. On the right of the page, each of the six textareas can be filled with a list of elements (one per line). If the same item is given multiple times, this one will be considered as unique. The list labels can also be customized using the text field on the top of each textarea.}\label{fig::web}  Jerome Mariette committed Aug 05, 2014 602  \end{figure}  Jerome Mariette committed Mar 03, 2014 603   Jerome Mariette committed Mar 20, 2014 604 605 606 607 608 609 610 611 612 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% %% %% Tables %% %% %% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %% Use of \listoftables is discouraged. %% \section*{Tables}  Jerome Mariette committed Jun 10, 2014 613 614  \begin{table}[h!]  Jerome Mariette committed Aug 05, 2014 615 616 \caption{Features of a subset of already available software packages, and jvenn.}\label{table::features}  Jerome Mariette committed Jun 10, 2014 617 618 619 620 621 622 623  \begin{tabular}{c|cccccc} Application & Maximum & Layouts & Application & Proportionality & Input data & Output\\ & number of & & type & & formats & formats \\ & input lists & & & & & \\ \hline VENNTURE \cite{Bronwen2012} & 6 & Edwards & Stand-alone & No & Lists &  Jerome Mariette committed Jun 11, 2014 624 625  Powerpoint\\ & & & & & & and Excel \\ \hline  Jerome Mariette committed Jun 10, 2014 626 627  VennDiagram \cite{RVennDiagram} & 5 & Classical & R package & No & Lists  Jerome Mariette committed Jun 11, 2014 628 629  & R object \\ & & & & & & and TIFF \\ \hline  Jerome Mariette committed Jun 10, 2014 630   Jerome Mariette committed Aug 05, 2014 631  BioVenn \cite{Hulsen2008} & 3 & Classical & web application & Yes &  Jerome Mariette committed Jun 11, 2014 632  Lists & SVG and PNG \\ \hline  Jerome Mariette committed Jun 10, 2014 633   Jerome Mariette committed Aug 05, 2014 634  venny \cite{venny} & 4 & Classical & web application & No &  Jerome Mariette committed Jun 10, 2014 635 636 637  Lists & PNG \\ \hline Canvasxpress \cite{canvasxpress} & 4 & Classical & JavaScript library &  Jerome Mariette committed Jun 11, 2014 638 639  No & Intersection & JavaScript \\ & & & & & counts & canvas \\ \hline  Jerome Mariette committed Jun 10, 2014 640 641 642  Google & 3 & Classical & JavaScript library & Yes & Lists & PNG \\  Jerome Mariette committed Jun 11, 2014 643  Chart API \cite{googleAPI} & & & & & & \\ \hline \hline  Jerome Mariette committed Jun 10, 2014 644   Jerome Mariette committed Aug 05, 2014 645  jvenn & 6 & Classical & web application & No & Lists,  Jerome Mariette committed Jun 10, 2014 646 647  & Interactive \\  Jerome Mariette committed Jun 11, 2014 648 649  & & and Edwards & and JavaScript & & intersection & diagram, \\ & & & library & & counts and & PNG and CSV \\  Jerome Mariette committed Jul 24, 2014 650  & & & & & Count lists &  Jerome Mariette committed Jun 10, 2014 651 652 653 654  \end{tabular} \end{table}  Jerome Mariette committed Mar 20, 2014 655 \begin{table}[h!]  Jerome Mariette committed Aug 05, 2014 656 \caption{Available input formats.}\label{table::format}  Jerome Mariette committed Mar 20, 2014 657 658  \begin{tabular}{cccc} \hline  Jerome Mariette committed Jul 24, 2014 659 660  Format & Example\\ \hline Lists &  Jerome Mariette committed Mar 20, 2014 661 662 663 664 665 666 667 668 669 \begin{lstlisting} series: [{ name: 'sample1', data: ["Otu1", "Otu2", "Otu3", "Otu4", "Otu5", "Otu6", "Otu7"] }, { name: 'sample2', data: ["Otu1", "Otu2", "Otu5", "Otu7", "Otu8", "Otu9"] }] \end{lstlisting}\\ \hline  Jerome Mariette committed Jul 24, 2014 670  Intersection counts &  Jerome Mariette committed Mar 20, 2014 671 672 \begin{lstlisting} series: [{  Jerome Mariette committed Jun 05, 2014 673 674  name: {A: 'sample 1', B: 'sample 2'}, data: {A: ["Otu3", "Otu4", "Otu6"], B: ["Otu8", "Otu9"], AB: ["Otu1",  Jerome Mariette committed Jun 11, 2014 675  "Otu2", "Otu5", "Otu7"]} }],  Jerome Mariette committed Jun 05, 2014 676  values: {A: 3, B: 2, AB: 4}  Jerome Mariette committed Mar 20, 2014 677 \end{lstlisting}\\ \hline  Jerome Mariette committed Jul 24, 2014 678  Count lists &  Jerome Mariette committed Mar 20, 2014 679 680 681 682 683 684 685 686 687 688 689 690 691 692 \begin{lstlisting} series: [{ name: 'sample1', data: ["Otu1", "Otu2", "Otu3", "Otu4", "Otu5", "Otu6", "Otu7"], values: [5, 15, 250, 20, 23, 58, 89] }, { name: 'sample2', data: ["Otu1", "Otu2", "Otu5", "Otu7", "Otu8", "Otu9"], values: [90, 300, 10, 2, 45, 9] }] \end{lstlisting}\\ \hline \end{tabular} \end{table}  Jerome Mariette committed Mar 03, 2014 693 \end{backmatter}  Jerome Mariette committed Mar 24, 2014 694 \end{document}