InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

BMC Bioinformatics - Tập 16 - Trang 1-7 - 2015
Henry Heberle1, Gabriela Vaz Meirelles2, Felipe R da Silva3, Guilherme P Telles4, Rosane Minghim1
1Universidade de São Paulo, Instituto de Ciências Matemáticas e de Computação, São Carlos, SP, Brazil
2Laboratório Nacional de Biociências, Campinas SP, Brazil
3Embrapa Informática Agropecuária, Campinas, SP, Brazil
4Universidade Estadual de Campinas, Instituto de Computação, Campinas SP, Brazil

Tóm tắt

Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited. We have developed InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are useful to reveal differences and similarities among sets and may be guided in our tool by a tree or by a list of set unions. The tool also allows obtaining subsets’ elements, saving and loading sets for further analyses, and exporting the diagram in vector and image formats. InteractiVenn has been used to analyze two biological datasets, but it may serve set analysis in a broad range of domains. InteractiVenn allows set unions in Venn diagrams to be explored thoroughly, by consequence extending the ability to analyze combinations of sets with additional observations, yielded by novel interactions between joined sets. InteractiVenn is freely available online at: www.interactivenn.net .

Tài liệu tham khảo

Ruskey F, Weston M. A survey of Venn diagrams. Electron J Comb. 1997; 4. D’Hont A, Denoeud F, Aury JM, et al. The banana (musa acuminata) genome and the evolution of monocotyledonous plants. Nature. 2012; 7410:213–7. Hulsen T, de Vlieg J, Alkema W. Biovenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. BMC Genomics. 2008; 9:488. Pirooznia M, Nagarajan V, Deng Y. GeneVenn - a web application for comparing gene lists using Venn diagrams. Bioinformation. 2007; 1(10):420–2. Kestler HA, Muller A, Gress TM, Buchholz M. Generalized Venn diagrams: a new method of visualizing complex genetic set relations. Bioinformatics. 2005; 21(5):1592–5. Bardou P, Mariette J, Escudié F, Djemiel C, Klopp C. jvenn : an interactive Venn diagram viewer. BMC Bioinformatics. 2014; 15(293):1–7. Martin B, Chadwick W, Yi T, et al. VENNTURE - a novel Venn diagram investigational tool for multiple pharmacological dataset analysis. PLos One. 2012; 7(5):1–17. Kim Y, Ignatchenko V, Yao CQ, et al. Identification of differentially expressed proteins in direct expressed prostatic secretions of men with organ-confined versus extracapsular prostate cancer. Mol Cell Proteomics. 2012; 11(12):1870–84. Kawahara R, Meirelles GV, Heberle H, et al. Integrative Analysis to Select Cancer Candidate Biomarkers to Targeted Validation. In revision. Pham T, Piersma S, Warmoes M, Jimenez C. On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics. Bioinformatics. 2010; 26(3):363–9. Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. PNAS. 2002; 99(10):6567–572. Guyon I, Weston J, Barnhill S, Vapnik V. A gene selection method for cancer classification using support vector machines. Mach Learn. 2002; 46(1-3):389–422. Christin C, Hoefsloot HCJ, Smilde AK, et al. A critical assessment of feature selection methods for biomarker discovery in clinical proteomics. Mol Cell Proteomics. 2013; 12(1):263–76.