BioVenn – a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams

By Tim Hulsen, J. de Vlieg, Wynand Alkema. BMC Genomics, 2008

1,563 citations recorded by the source corpus.

BackgroundIn many genomics projects, numerous lists containing biological identifiers are produced. Often it is useful to see the overlap between different lists, enabling researchers to quickly observe similarities and differences between the data sets they are analyzing. One of the most popular methods to visualize the overlap and differences between data sets is the Venn diagram: a diagram consisting of two or more circles in which each circle corresponds to a data set, and the overlap between the circles corresponds to the overlap between the data sets. Venn diagrams are especially useful when they are 'area-proportional' i.e. the sizes of the circles and the overlaps correspond to the sizes of the data sets. Currently there are no programs available that can create area-proportional Venn diagrams connected to a wide range of biological databases.ResultsWe designed a web application named BioVenn to summarize the overlap between two or three lists of identifiers, using area-proportional Venn diagrams. The user only needs to input these lists of identifiers in the textboxes and push the submit button. Parameters like colors and text size can be adjusted easily through the web interface. The position of the text can be adjusted by 'drag-and-drop' principle. The output Venn diagram can be shown as an SVG or PNG image embedded in the web application, or as a standalone SVG or PNG image. The latter option is useful for batch queries. Besides the Venn diagram, BioVenn outputs lists of identifiers for each of the resulting subsets. If an identifier is recognized as belonging to one of the supported biological databases, the output is linked to that database. Finally, BioVenn can map Affymetrix and EntrezGene identifiers to Ensembl genes.ConclusionBioVenn is an easy-to-use web application to generate area-proportional Venn diagrams from lists of biological identifiers. It supports a wide range of identifiers from the most used biological databases currently available. Its implementation on the World Wide Web makes it available for use on any computer with internet connection, independent of operating system and without the need to install programs locally. BioVenn is freely accessible at http://www.cmbi.ru.nl/cdd/biovenn/.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/efbb419f298d8d99f1728a45bea82b19fefffb90

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R (2011, methodology): “Other, non-R-based local or web-based software capable of generating Venn diagrams exist, such as Venny [5], BioVenn [6], ConSet [7], and VennMaster [8].”
jvenn: an interactive Venn diagram viewer (2014, methodology): “BioVenn [5] 3 Classical web application Yes Lists SVG and PNG”
OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes (2013, methodology): “Venn diagrams were created with the BioVenn application (Hulsen et al., 2008).”
OrthoVenn: a web server for genome wide comparison and annotation of orthologous clusters across multiple species (2015, methodology): “BioVenn (13) provides a comparison and visualization of biological lists using area-proportional Venn diagrams.”
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets (2017, methodology): “BioVenn [10] Classical Venn web app Lists 3 SVG, PNG”
eulerAPE: Drawing Area-Proportional 3-Venn Diagrams Using Ellipses (2014, methodology): “A few of these methods and examples of diagrams drawn using them, include: BioVenn [38] (e.g., Figure 3-C5, [39]); Venn Diagram Plotter [http://omics.pnl.gov/software/VennDiagramPlotter. php] (e.g., Figure 1C, Figure 3-C2, [13]); a module in PatternLab for proteomics [40] (e.g., Figure 3-C4, [41]);…”
InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams (2015, background): “Other examples are DrawVenn (http://bioinformatics.psb.ugent.be/webtools/ Venn/) and BioVenn [3] that construct area-proportional diagrams, limited by the fact that it is not possible to create symmetric Venn diagrams with more than four sets that respect proportionality.”
Transient leaf endophytes are the most active fungi in 1-year-old beech leaf litter (2017, methodology): “Area-proportional Euler Diagrams were generated using the BioVenn web application (Hulsen et al. 2008).”
Cytoplasmic 5′-3′ exonuclease Xrn1p is also a genome-wide transcription factor in yeast (2013, methodology): “Venn diagrams were drawn using the online BioVenn tool (Hulsen et al., 2008).”