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      VennPainter: A Tool for the Comparison and Identification of Candidate Genes Based on Venn Diagrams

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          Abstract

          VennPainter is a program for depicting unique and shared sets of genes lists and generating Venn diagrams, by using the Qt C++ framework. The software produces Classic Venn, Edwards’ Venn and Nested Venn diagrams and allows for eight sets in a graph mode and 31 sets in data processing mode only. In comparison, previous programs produce Classic Venn and Edwards’ Venn diagrams and allow for a maximum of six sets. The software incorporates user-friendly features and works in Windows, Linux and Mac OS. Its graphical interface does not require a user to have programing skills. Users can modify diagram content for up to eight datasets because of the Scalable Vector Graphics output. VennPainter can provide output results in vertical, horizontal and matrix formats, which facilitates sharing datasets as required for further identification of candidate genes. Users can obtain gene lists from shared sets by clicking the numbers on the diagram. Thus, VennPainter is an easy-to-use, highly efficient, cross-platform and powerful program that provides a more comprehensive tool for identifying candidate genes and visualizing the relationships among genes or gene families in comparative analysis.

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          clusterMaker: a multi-algorithm clustering plugin for Cytoscape

          John H. Morris, Leonard Apeltsin, Aaron Newman … (2011)
          Background In the post-genomic era, the rapid increase in high-throughput data calls for computational tools capable of integrating data of diverse types and facilitating recognition of biologically meaningful patterns within them. For example, protein-protein interaction data sets have been clustered to identify stable complexes, but scientists lack easily accessible tools to facilitate combined analyses of multiple data sets from different types of experiments. Here we present clusterMaker, a Cytoscape plugin that implements several clustering algorithms and provides network, dendrogram, and heat map views of the results. The Cytoscape network is linked to all of the other views, so that a selection in one is immediately reflected in the others. clusterMaker is the first Cytoscape plugin to implement such a wide variety of clustering algorithms and visualizations, including the only implementations of hierarchical clustering, dendrogram plus heat map visualization (tree view), k-means, k-medoid, SCPS, AutoSOME, and native (Java) MCL. Results Results are presented in the form of three scenarios of use: analysis of protein expression data using a recently published mouse interactome and a mouse microarray data set of nearly one hundred diverse cell/tissue types; the identification of protein complexes in the yeast Saccharomyces cerevisiae; and the cluster analysis of the vicinal oxygen chelate (VOC) enzyme superfamily. For scenario one, we explore functionally enriched mouse interactomes specific to particular cellular phenotypes and apply fuzzy clustering. For scenario two, we explore the prefoldin complex in detail using both physical and genetic interaction clusters. For scenario three, we explore the possible annotation of a protein as a methylmalonyl-CoA epimerase within the VOC superfamily. Cytoscape session files for all three scenarios are provided in the Additional Files section. Conclusions The Cytoscape plugin clusterMaker provides a number of clustering algorithms and visualizations that can be used independently or in combination for analysis and visualization of biological data sets, and for confirming or generating hypotheses about biological function. Several of these visualizations and algorithms are only available to Cytoscape users through the clusterMaker plugin. clusterMaker is available via the Cytoscape plugin manager.
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            Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways.

            Nicholas R. Thomson, Debra J Clayton, Daniel Windhorst … (2008)
            We have determined the complete genome sequences of a host-promiscuous Salmonella enterica serovar Enteritidis PT4 isolate P125109 and a chicken-restricted Salmonella enterica serovar Gallinarum isolate 287/91. Genome comparisons between these and other Salmonella isolates indicate that S. Gallinarum 287/91 is a recently evolved descendent of S. Enteritidis. Significantly, the genome of S. Gallinarum has undergone extensive degradation through deletion and pseudogene formation. Comparison of the pseudogenes in S. Gallinarum with those identified previously in other host-adapted bacteria reveals the loss of many common functional traits and provides insights into possible mechanisms of host and tissue adaptation. We propose that experimental analysis in chickens and mice of S. Enteritidis-harboring mutations in functional homologs of the pseudogenes present in S. Gallinarum could provide an experimentally tractable route toward unraveling the genetic basis of host adaptation in S. enterica.
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              Visualization of comparative genomic analyses by BLAST score ratio

              David Rasko, Garry Myers, Jacques Ravel (2005)
              Background The first microbial genome sequence, Haemophilus influenzae, was published in 1995. Since then, more than 400 microbial genome sequences have been completed or commenced. This massive influx of data provides the opportunity to obtain biological insights through comparative genomics. However few tools are available for this scale of comparative analysis. Results The BLAST Score Ratio (BSR) approach, implemented in a Perl script, classifies all putative peptides within three genomes using a measure of similarity based on the ratio of BLAST scores. The output of the BSR analysis enables global visualization of the degree of proteome similarity between all three genomes. Additional output enables the genomic synteny (conserved gene order) between each genome pair to be assessed. Furthermore, we extend this synteny analysis by overlaying BSR data as a color dimension, enabling visualization of the degree of similarity of the peptides being compared. Conclusions Combining the degree of similarity, synteny and annotation will allow rapid identification of conserved genomic regions as well as a number of common genomic rearrangements such as insertions, deletions and inversions. The script and example visualizations are available at: .
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                Author and article information

                Contributors
                Nicholas J. Provart: Role: Editor
                Journal
                Journal ID (nlm-ta): PLoS One
                Journal ID (iso-abbrev): PLoS ONE
                Journal ID (publisher-id): plos
                Journal ID (pmc): plosone
                Title: PLoS ONE
                Publisher: Public Library of Science (San Francisco, CA USA )
                ISSN (Electronic): 1932-6203
                Publication date (Electronic): 27 April 2016
                Publication date Collection: 2016
                Volume: 11
                Issue: 4
                Electronic Location Identifier: e0154315
                Affiliations
                [1 ]Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, School of Life Sciences, Yunnan University, Kunming, 650091, China
                [2 ]School of Software, Yunnan University, Kunming, 650091, Yunnan, China
                [3 ]State Key Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, 650091, Yunnan, China
                [4 ]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, The Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
                [5 ]Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650000, China
                [6 ]Centre for Biodiversity and Conservation Biology, Royal Ontario Museum, Toronto, M5S 2C6, Canada
                [7 ]School of Computer and Science, Fudan University, Shanghai, 200433, China
                University of Toronto, CANADA
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: WZ JL. Performed the experiments: GLL. Analyzed the data: GLL JC. Contributed reagents/materials/analysis tools: SY CM LC WZ. Wrote the paper: GLL JC JL. Revised the manuscript: RM WZ JL.

                Article
                Publisher ID: PONE-D-15-50932
                DOI: 10.1371/journal.pone.0154315
                PMC ID: 4847855
                PubMed ID: 27120465
                SO-VID: 1435f4a1-606c-412c-b996-90f1e0a1a1a0
                Copyright © © 2016 Lin et al
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                Date received : 22 November 2015
                Date accepted : 12 April 2016
                Page count
                Figures: 6, Tables: 1, Pages: 12
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 91331105
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 31360514
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 61363021
                Award Recipient :
                This research was supported by the National Natural Science Foundation of China (91331105, 31360514 and 61363021), Program for Innovative Research Team (in Science and Technology) in University of Yunnan Province, and the State Key laboratory of Genetics, Resources and Evolution, Kunming Institute of Zoology, CAS. The funders JL and WZ (three projects of the National Natural Science Foundation of China) conceived and designed the study. The other funders (the last two projects in the above list) had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Subject: Research Article
                Subject: Engineering and Technology
                Subject: Human Factors Engineering
                Subject: Man-Computer Interface
                Subject: Graphical User Interface
                Subject: Computer and Information Sciences
                Subject: Computer Architecture
                Subject: User Interfaces
                Subject: Graphical User Interface
                Subject: Computer and Information Sciences
                Subject: Computer Software
                Subject: Computer and Information Sciences
                Subject: Computer Architecture
                Subject: User Interfaces
                Subject: Computer and Information Sciences
                Subject: Computer Applications
                Subject: Web-Based Applications
                Subject: Biology and Life Sciences
                Subject: Organisms
                Subject: Animals
                Subject: Vertebrates
                Subject: Amniotes
                Subject: Mammals
                Subject: Primates
                Subject: Computer and Information Sciences
                Subject: Data Visualization
                Subject: Infographics
                Subject: Graphs
                Subject: Computer and Information Sciences
                Subject: Information Technology
                Subject: Data Processing
                Subject: Biology and Life Sciences
                Subject: Computational Biology
                Subject: Comparative Genomics
                Subject: Biology and Life Sciences
                Subject: Genetics
                Subject: Genomics
                Subject: Comparative Genomics
                Custom metadata
                Data Availability VennPainter is available on https://github.com/linguoliang/VennPainter/, The GFF files are downloaded from NCBI genome database.

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