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DynaVenn: web-based computation of the most significant overlap between ordered sets.
Jérémy Amand1, Tobias Fehlmann1, Christina Backes1
1Chair for Clinical Bioinformatics, Saarland University, Saarbrücken, 66123, DE, Germany.
BMC Bioinformatics
|January 1, 2020
Summary
DynaVenn, a new tool, identifies the most significant overlaps between ordered gene lists from different studies. It visualizes these findings dynamically, improving upon fixed threshold comparisons.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Ordered lists are frequently compared in research, such as gene or protein significance lists between primary and replication studies.
- Direct comparison using fixed thresholds can be misleading due to variations in cohort size or evaluation methods.
- Euler diagrams (Venn diagrams) are often used but may not be optimal for complex list comparisons.
Purpose of the Study:
- To develop a novel web-based tool, DynaVenn, for comparing ordered lists.
- To provide a method for identifying the most significant overlap between two or three ordered lists.
- To offer an intuitive visualization of comparative list analysis results.
Main Methods:
- DynaVenn incrementally generates all possible subsets from two or three ordered lists.
- It computes a p-value for the overlap of each subset.
- Dynamic Venn diagrams and backtracking animations visualize the results.
Main Results:
- DynaVenn successfully identifies significant overlaps in ordered lists.
- The tool demonstrated improved performance over arbitrary cut-off methods using an Alzheimer's Disease biomarker set.
- Dynamic visualizations aid in understanding how significant overlaps are achieved.
Conclusions:
- DynaVenn offers a robust method for calculating and visualizing the most significant overlaps between different cohorts.
- The tool provides an intuitive graphical representation of complex comparative analyses.
- DynaVenn is available as a free web service.
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