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

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          Abstract

          Background

          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.

          Results

          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.

          Conclusions

          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.

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          Most cited references8

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          New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily

          Background The Acel_2062 protein from Acidothermus cellulolyticus is a protein of unknown function. Initial sequence analysis predicted that it was a metallopeptidase from the presence of a motif conserved amongst the Asp-zincins, which are peptidases that contain a single, catalytic zinc ion ligated by the histidines and aspartic acid within the motif (HEXXHXXGXXD). The Acel_2062 protein was chosen by the Joint Center for Structural Genomics for crystal structure determination to explore novel protein sequence space and structure-based function annotation. Results The crystal structure confirmed that the Acel_2062 protein consisted of a single, zincin-like metallopeptidase-like domain. The Met-turn, a structural feature thought to be important for a Met-zincin because it stabilizes the active site, is absent, and its stabilizing role may have been conferred to the C-terminal Tyr113. In our crystallographic model there are two molecules in the asymmetric unit and from size-exclusion chromatography, the protein dimerizes in solution. A water molecule is present in the putative zinc-binding site in one monomer, which is replaced by one of two observed conformations of His95 in the other. Conclusions The Acel_2062 protein is structurally related to the zincins. It contains the minimum structural features of a member of this protein superfamily, and can be described as a “mini- zincin”. There is a striking parallel with the structure of a mini-Glu-zincin, which represents the minimum structure of a Glu-zincin (a metallopeptidase in which the third zinc ligand is a glutamic acid). Rather than being an ancestral state, phylogenetic analysis suggests that the mini-zincins are derived from larger proteins.
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            Erratum: gene selection for cancer classification using support vector machines

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              GeneVenn - A web application for comparing gene lists using Venn diagrams

              Numerous methods are available to compare results of multiple microarray studies. One of the simplest but most effective of these procedures is to examine the overlap of resulting gene lists in a Venn diagram. Venn diagrams are graphical ways of representing interactions among sets to display information that can be read easily. Here we propose a simple but effective web application creating Venn diagrams from two or three gene lists. Each gene in the group list has link to the related information in NCBI's Entrez Nucleotide database. Availability GeneVenn is available for free at http://mcbc.usm.edu/genevenn/
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                Author and article information

                Contributors
                henry@icmc.usp.br
                gabriela.meirelles@lnbio.cnpem.br
                felipe.silva@embrapa.br
                gpt@ic.unicamp.br
                rminghim@icmc.usp.br
                Journal
                BMC Bioinformatics
                BMC Bioinformatics
                BMC Bioinformatics
                BioMed Central (London )
                1471-2105
                22 May 2015
                22 May 2015
                2015
                : 16
                : 1
                : 169
                Affiliations
                [ ]Universidade de São Paulo, Instituto de Ciências Matemáticas e de Computação, Av. Trabalhador São-carlense, 400, São Carlos SP, Brazil
                [ ]Laboratório Nacional de Biociências, Campinas SP, Caixa Postal 6192 Brazil
                [ ]Embrapa Informática Agropecuária, Av. André Tosello, 209, Campinas SP, Brazil
                [ ]Universidade Estadual de Campinas, Instituto de Computação, Av. Albert Einstein, 1251, Campinas SP, Brazil
                Article
                611
                10.1186/s12859-015-0611-3
                4455604
                25994840
                2f9ba3ec-841b-4a87-8bc6-70873bcd1479
                © Heberle et al.; licensee BioMed Central. 2015

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 28 January 2015
                : 6 May 2015
                Categories
                Software
                Custom metadata
                © The Author(s) 2015

                Bioinformatics & Computational biology
                venn diagram,edwards-venn diagram,interaction,set-unions

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