Generalized Venn diagrams: a new method of visualizing complex genetic set relations

Bioinformatics
Hans A KestlerMalte Buchholz

Abstract

Microarray experiments generate vast amounts of data. The unknown or only partially known functional context of differentially expressed genes may be assessed by querying the Gene Ontology database via GOMiner. Resulting tree representations are difficult to interpret and are not suited for visualization of this type of data. Methods are needed to effectively visualize these complex set relationships. We present a visualization approach for set relationships based on Venn diagrams. The proposed extension enhances the usual notion of Venn diagrams by incorporating set size information. The cardinality of the sets and intersection sets is represented by their corresponding circle (polygon) sizes. To avoid local minima, solutions to this problem are sought by evolutionary optimization. This generalized Venn diagram approach has been implemented as an interactive Java application (VennMaster) specifically designed for use with GOMiner in the context of the Gene Ontology database. VennMaster is platform-independent (Java 1.4.2) and has been tested on Windows (XP, 2000), Mac OS X, and Linux. Supplementary information and the software (free for non-commercial use) are available at http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestl...Continue Reading

Associated Proceedings Papers

References

Dec 1, 2007·Interacting with Computers·Bohyoung KimJinwook Seo
Feb 23, 2008·Bioinformatics·Bongshin LeeJinwook Seo
Oct 10, 2006·Journal of Bacteriology·Aldert L ZomerOscar P Kuipers
Jan 31, 2008·BMC Bioinformatics·Hans A KestlerJohn N Weinstein
Jun 24, 2009·Plant Methods·James C Estill, Jeffrey L Bennetzen
Apr 2, 2011·BMC Medical Genomics·Trevor ClancyEivind Hovig
Jul 18, 2014·PloS One·Luana Micallef, Peter Rodgers
Jun 29, 2007·Bioinformation·Mehdi PiroozniaYouping Deng
Apr 29, 2014·Nucleic Acids Research·Yi WangYong Q Gu
Sep 11, 2014·The Journal of Investigative Dermatology·Claire da Silva SantosSerhiy Souchelnytskyi
Feb 14, 2007·Trends in Ecology & Evolution·Jan E KammengaRainer Breitling
Jun 20, 2015·Molecular Cell·Casey M DanielsAnthony K L Leung
Sep 20, 2015·Human Genetics·Jörn LötschAlfred Ultsch
Mar 21, 2008·International Journal of Cancer. Journal International Du Cancer·Selvaraju VeeriahBeatrice Louise Pool-Zobel
May 12, 2012·IEEE Transactions on Visualization and Computer Graphics·Peter RodgersHelen Purchase
Mar 9, 2011·IEEE Transactions on Visualization and Computer Graphics·Leland Wilkinson
Nov 8, 2008·IEEE Transactions on Visualization and Computer Graphics·Wolfgang FreilerHelwig Hauser
Nov 13, 2010·IEEE Transactions on Visualization and Computer Graphics·Gem StapletonLeishi Zhang
Nov 26, 2015·Scientific Reports·Minghui WangBin Zhang
Apr 16, 2013·Journal of the American Academy of Child and Adolescent Psychiatry·Matthew F PescosolidoEric M Morrow
Oct 12, 2010·Plant Signaling & Behavior·Carmen Bianco, Roberto Defez
May 23, 2015·BMC Bioinformatics·Henry HeberleRosane Minghim
Nov 1, 2016·Journal of Virology·Bart M MaślikowskiPierre-André Bédard
Apr 23, 2017·Neurology·Tobias BobingerMartin Köhrmann
Sep 29, 2007·Molecular Endocrinology·Hui GaoKarin Dahlman-Wright
Sep 6, 2019·Scientific Reports·Hans KubitschkeJosef Käs
Oct 26, 2018·BMC Bioinformatics·Rolf HühneHans A Kestler

Citations

Apr 19, 2003·Genome Biology·Barry R ZeebergJohn N Weinstein

Related Concepts

Computer Graphics
Logistic Regression
Computer Programs and Programming
Virtual Systems
Cdna Microarrays
Evolution, Molecular
Gene Ontology
MRNA Differential Display
Opitz-Frias Syndrome

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Sexual Dimorphism in Neurodegeneration

There exist sex differences in neurodevelopmental and neurodegenerative disorders. For instance, multiple sclerosis is more common in women, whereas Parkinson’s disease is more common in men. Here is the latest research on sexual dimorphism in neurodegeneration

HLA Genetic Variation

HLA genetic variation has been found to confer risk for a wide variety of diseases. Identifying these associations and understanding their molecular mechanisms is ongoing and holds promise for the development of therapeutics. Find the latest research on HLA genetic variation here.

Super-resolution Microscopy

Super-resolution microscopy is the term commonly given to fluorescence microscopy techniques with resolutions that are not limited by the diffraction of light. Here are the latest discoveries pertaining to super-resolution microscopy.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells.

Brain Lower Grade Glioma

Low grade gliomas in the brain form from oligodendrocytes and astrocytes and are the slowest-growing glioma in adults. Discover the latest research on these brain tumors here.

CD4/CD8 Signaling

Cluster of differentiation 4 and 8 (CD8 and CD8) are glycoproteins founds on the surface of immune cells. Here is the latest research on their role in cell signaling pathways.

Alignment-free Sequence Analysis Tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.