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DynaVenn: web-based computation of the most significant overlap between ordered sets

Authors
  • Amand, Jérémy1
  • Fehlmann, Tobias1
  • Backes, Christina1
  • Keller, Andreas1
  • 1 Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, DE, 66123, Germany , Saarbrücken (Germany)
Type
Published Article
Journal
BMC Bioinformatics
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Dec 30, 2019
Volume
20
Issue
1
Identifiers
DOI: 10.1186/s12859-019-3320-5
Source
Springer Nature
Keywords
License
Green

Abstract

BackgroundIn many research disciplines, ordered lists are compared. One example is to compare a subset of all significant genes or proteins in a primary study to those in a replication study. Often, the top of the lists are compared using Venn diagrams, ore more precisely Euler diagrams (set diagrams showing logical relations between a finite collection of different sets). If different cohort sizes, different techniques or algorithms for evaluation were applied, a direct comparison of significant genes with a fixed threshold can however be misleading and approaches comparing lists would be more appropriate.ResultsWe developed DynaVenn, a web-based tool that incrementally creates all possible subsets from two or three ordered lists and computes for each combination a p-value for the overlap. Respectively, dynamic Venn diagrams are generated as graphical representations. Additionally an animation is generated showing how the most significant overlap is reached by backtracking. We demonstrate the improved performance of DynaVenn over an arbitrary cut-off approach on an Alzheimer’s Disease biomarker set.ConclusionDynaVenn combines the calculation of the most significant overlap of different cohorts with an intuitive visualization of the results. It is freely available as a web service at http://www.ccb.uni-saarland.de/dynavenn.

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