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

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.     

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

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.     

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/     

VennDIS: A JavaFX‐based Venn and Euler diagram software to generate publication quality figures

Venn diagrams are graphical representations of the relationships among multiple sets of objects and are often used to illustrate similarities and differences among genomic and proteomic datasets. All currently existing tools for producing Venn diagrams evince one of two traits; they require expertise in specific statistical software packages (such as R), or lack the flexibility required to produce publication‐quality figures. We describe a simple tool that addresses both shortcomings, Venn Diagram Interactive Software (VennDIS), a JavaFX‐based solution for producing highly customizable, publication‐quality Venn, and Euler diagrams of up to five sets. The strengths of VennDIS are its simple graphical user interface and its large array of customization options, including the ability to modify attributes such as font, style and position of the labels, background color, size of the circle/ellipse, and outline color. It is platform independent and provides real‐time visualization of figure modifications. The created figures can be saved as XML files for future modification or exported as high‐resolution images for direct use in publications.     

Generalized Venn diagrams: a new method of visualizing complex genetic set relations

MOTIVATION: Microarray experiments generate vast amounts of data. The unknown or only partially known functional context of differentially expressed genes may be assessed by querying the Gene Ontology database via GOMiner. Resulting tree representations are difficult to interpret and are not suited for visualization of this type of data. Methods are needed to effectively visualize these complex set relationships. RESULTS: We present a visualization approach for set relationships based on Venn diagrams. The proposed extension enhances the usual notion of Venn diagrams by incorporating set size information. The cardinality of the sets and intersection sets is represented by their corresponding circle (polygon) sizes. To avoid local minima, solutions to this problem are sought by evolutionary optimization. This generalized Venn diagram approach has been implemented as an interactive Java application (VennMaster) specifically designed for use with GOMiner in the context of the Gene Ontology database. AVAILABILITY: VennMaster is platform-independent (Java 1.4.2) and has been tested on Windows (XP, 2000), Mac OS X, and Linux. Supplementary information and the software (free for non-commercial use) are available at http://www.informatik.uni-ulm.de/ni/mitarbeiter/HKestler/vennm together with a user documentation. CONTACT: hans.kestler@medizin.uni-ulm.de.     

jvenn: an interactive Venn diagram viewer

Background

Venn diagrams are commonly used to display list comparison. In biology, they are widely used to show the differences between gene lists originating from different differential analyses, for instance. They thus allow the comparison between different experimental conditions or between different methods. However, when the number of input lists exceeds four, the diagram becomes difficult to read. Alternative layouts and dynamic display features can improve its use and its readability.

Results

jvenn is a new JavaScript library. It processes lists and produces Venn diagrams. It handles up to six input lists and presents results using classical or Edwards-Venn layouts. User interactions can be controlled and customized. Finally, jvenn can easily be embeded in a web page, allowing to have dynamic Venn diagrams.

Conclusions

jvenn is an open source component for web environments helping scientists to analyze their data. The library package, which comes with full documentation and an example, is freely available at http://bioinfo.genotoul.fr/jvenn.     

The visual perception of the ant Myrmica ruginodis (Hymenoptera: Formicidae)

Myrmica ruginodis workers are able to distinguish black or white circles from black or white squares, black or white ellipses from black or white rectangles as well as hollow circles or ellipses from hollow squares or rectangles. They can also distinguish differently oriented elements as well as objects containing a various number of elements. These workers are also able to perceive and discriminate transparent cues on a black background and even small luminous spots on a black ceiling. Such visual abilities are in agreement with the species?? eye morphology and system of navigation: the eyes are rather large with a well-developed posterio-dorsal part, and the foragers rely exclusively on cues located above them, neglecting odorous elements as long as visual perception is possible. Probably, they might use cues located in the canopy and the sky to travel in certain circumstances.     

Spatial modelling-based approach to phytogeographical regionalization using grassland vegetation data

We presented a methodology for drawing continuous boundaries in the landscape differentiating between regions with different floristic composition. A region in Central Slovakia covering 2,445 km² was investigated. Ecological indicator values for temperature (EIT) in 1,978 grassland polygons were analysed. Ordinary kriging was used to interpolate EIT across the study region. Lattice wombling was used to identify the most intensive gradients in EIT and to draw boundaries, while ANOVA was used for post-classification analysis. A strong pattern of spatial continuity was present in EIT assigned to species in grassland polygons allowing for drawing continuous boundaries in the landscape. The study region was divided into 15 districts using the proposed method. Post-classification analysis indicated that 17 out of 23 adjacent districts were found to differ significantly in term of mean value of source samples. The results implied the need for incorporating spatial autocorrelation in sample data into post-classification analysis; such factor is often neglected in ecological research. The presented findings suggested broader applicability of the proposed method for spatial modelling, as vegetation data is widely accessible in databases for many regions of Europe.     

VENNTURE--a novel Venn diagram investigational tool for multiple pharmacological dataset analysis

As pharmacological data sets become increasingly large and complex, new visual analysis and filtering programs are needed to aid their appreciation. One of the most commonly used methods for visualizing biological data is the Venn diagram. Currently used Venn analysis software often presents multiple problems to biological scientists, in that only a limited number of simultaneous data sets can be analyzed. An improved appreciation of the connectivity between multiple, highly-complex datasets is crucial for the next generation of data analysis of genomic and proteomic data streams. We describe the development of VENNTURE, a program that facilitates visualization of up to six datasets in a user-friendly manner. This program includes versatile output features, where grouped data points can be easily exported into a spreadsheet. To demonstrate its unique experimental utility we applied VENNTURE to a highly complex parallel paradigm, i.e. comparison of multiple G protein-coupled receptor drug dose phosphoproteomic data, in multiple cellular physiological contexts. VENNTURE was able to reliably and simply dissect six complex data sets into easily identifiable groups for straightforward analysis and data output. Applied to complex pharmacological datasets, VENNTURE's improved features and ease of analysis are much improved over currently available Venn diagram programs. VENNTURE enabled the delineation of highly complex patterns of dose-dependent G protein-coupled receptor activity and its dependence on physiological cellular contexts. This study highlights the potential for such a program in fields such as pharmacology, genomics, and bioinformatics.     

Preliminary study on the phytochemical evolution of different Lamiaceae species based on iridoids

In this work, an interesting potential application of phytochemistry is reported. In particular, we employed the Sporne diagrams to provide information about the evolution of some different Lamiaceae species in relation to their content in secondary metabolites. In more details, fifteen species belonging to six different genera were studied i.e. Ajuga L., Galeopsis L., Melittis L., Sideritis L., Stachys L. and Teucrium L. The selected secondary metabolites were iridoids because of their wide occurrence and distribution within all the family, thus providing a more accurate and general overview. Nineteen different compounds of this class were identified in the studied species. The aim of this work was to verify if the evolutionary data available in literature for the studied species and based on molecular studies, matched with those obtained from a more phytochemical approach or not. The final objective was to ascertain a correspondence between these two opposite methods. The results of this study clearly showed that, only in some cases, this correspondence was present. This may suggest the possibility to use both methods for drawing phylogenetic trees of plants. Anyway, this study is not general and is quite limited in studied species and in collection areas and does not intend to affirm its absolute accuracy even though it may be a good starting point for future researches in this field.     

Local false discovery rate facilitates comparison of different microarray experiments

The local false discovery rate (LFDR) estimates the probability of falsely identifying specific genes with changes in expression. In computer simulations, LFDR <10% successfully identified genes with changes in expression, while LFDR >90% identified genes without changes. We used LFDR to compare different microarray experiments quantitatively: (i) Venn diagrams of genes with and without changes in expression, (ii) scatter plots of the genes, (iii) correlation coefficients in the scatter plots and (iv) distributions of gene function. To illustrate, we compared three methods for pre-processing microarray data. Correlations between methods were high (r = 0.84–0.92). However, responses were often different in magnitude, and sometimes discordant, even though the methods used the same raw data. LFDR complements functional assessments like gene set enrichment analysis. To illustrate, we compared responses to ultraviolet radiation (UV), ionizing radiation (IR) and tobacco smoke. Compared to unresponsive genes, genes responsive to both UV and IR were enriched for cell cycle, mitosis, and DNA repair functions. Genes responsive to UV but not IR were depleted for cell adhesion functions. Genes responsive to tobacco smoke were enriched for detoxification functions. Thus, LFDR reveals differences and similarities among experiments.     

Accounting for space and uncertainty in real‐time location system‐derived contact networks

1. Point data obtained from real‐time location systems (RTLSs) can be processed into animal contact networks, describing instances of interaction between tracked individuals. Proximity‐based definitions of interanimal “contact,” however, may be inadequate for describing epidemiologically and sociologically relevant interactions involving body parts or other physical spaces relatively far from tracking devices. This weakness can be overcome by using polygons, rather than points, to represent tracked individuals and defining “contact” as polygon intersections.
2. We present novel procedures for deriving polygons from RTLS point data while maintaining distances and orientations associated with individuals' relocation events. We demonstrate the versatility of this methodology for network modeling using two contact network creation examples, wherein we use this procedure to create (a) interanimal physical contact networks and (b) a visual contact network. Additionally, in creating our networks, we establish another procedure to adjust definitions of “contact” to account for RTLS positional accuracy, ensuring all true contacts are likely captured and represented in our networks.
3. Using the methods described herein and the associated R package we have developed, called contact, researchers can derive polygons from RTLS points. Furthermore, we show that these polygons are highly versatile for contact network creation and can be used to answer a wide variety of epidemiological, ethological, and sociological research questions.
4. By introducing these methodologies and providing the means to easily apply them through the contact R package, we hope to vastly improve network‐model realism and researchers' ability to draw inferences from RTLS data.

     

Determination of age at death in human skeletal remains: A comparison of two techniques

Reliable palaeodemographic reconstruction is dependent upon accurate determination of age at death in human skeletal remains. Two methods, Todd (Todd, 1920, 1921) and Suchey-Brooks (Katz & Suchey, 1986), which use morphological changes of theos pubis as an indicator of age at death, were applied to a sample of Central California Indians. Life tables were constructed and the two data sets were compared. Differences between the two data sets were evident when life expectancies, mean ages, and survivorship curves were compared. Because both methods were developed using male samples, only the male data were considered valid. In a comparison between the two male data sets it became apparent that the differences lie in the upper decades depending upon which method was used. In an attempt to rectify the difference in age ranges between the two methods, a conversion of Todd phases into equivalent Suchey-Brooks phases (Katz & Suchey, 1986) was employed. Applications and limitations of both methods are discussed and it is suggested that the Suchey-Brooks method is to be perferred.     

Sensorimotor transformations underlying the organization of arm movements in three-dimensional space

Coordinated movements in three-dimensional space involve sensorimotor transformations between extrinsic and intrinsic coordinates. It is hypothesized that a key aspect underlying the organization of such movements is the need to simplify these transformations by means of suitable approximations and the imposition of constraints. Motor tasks involving the drawing of circles and ellipses in different planes were analyzed from this perspective, and some rules are presented whereby the plane of motion and the slant of an ellipse can be specified in a simple way in terms of intrinsic parameters. It is shown that these rules can be generalized to hold for more complicated wrist motions if one assumes that they consist of segments of elliptical arcs.     

Pollution Impacts on Bacterioplankton Diversity in a Tropical Urban Coastal Lagoon System

Despite a great number of published studies addressing estuarine, freshwater and marine bacterial diversity, few have examined urban coastal lagoons in tropical habitats. There is an increasing interest in monitoring opportunistic pathogens as well as indigenous microbial community members in these water bodies by current molecular and microbiological approaches. In this work, bacterial isolates were obtained through selective plate dilution methods to evaluate antibiotic resistances. In addition, 16S rRNA gene libraries were prepared from environmental waters and mixed cultures grown in BHI medium inoculated with Jacarepaguá lagoon waters. Denaturing gradient gel electrophoresis (DGGE) analyses showed distinct community profiles between environmental communities from each studied site and their cultured counterparts. A total of 497 bacterial sequences were analyzed by MOTHUR, yielding 245 operational taxonomic units (OTUs) grouped at 97% similarity. CCA diagrams showcased how several environmental variables affect the distribution of 18 bacterial orders throughout the three distinct habitats. UniFrac metrics and Venn diagrams revealed that bacterial communities retrieved through each experimental approach were significantly different and that only one OTU, closely related to Vibrio cholerae, was shared between them. Potentially pathogenic bacteria were isolated from most sampled environments, fifty percent of which showed antibiotic resistance.     

Implementation and evaluation of relative and absolute quantification in shotgun proteomics with label-free methods

Tandem mass spectrometry allows for fast protein identification in a complex sample. As mass spectrometers get faster, more sensitive and more accurate, methods were devised by many academic research groups and commercial suppliers that allow protein research also in quantitative respect. Since label-free methods are an attractive alternative to labeling approaches for proteomics researchers seeking for accurate quantitative results we evaluated several open-source analysis tools in terms of performance on two reference data sets, explicitly generated for this purpose.In this paper we present an implementation, T3PQ (Top 3 Protein Quantification), of the method suggested by Silva and colleagues for LC-MS^E applications and we demonstrate its applicability to data generated on FT-ICR instruments acquiring in data dependent acquisition (DDA) mode. In order to validate this method and to show its usefulness also for absolute protein quantification, we generated a reference data set of a sample containing four different proteins with known concentrations. Furthermore, we compare three other label-free quantification methods using a complex biological sample spiked with a standard protein in defined concentrations. We evaluate the applicability of these methods and the quality of the results in terms of robustness and dynamic range of the spiked-in protein as well as other proteins also detected in the mixture. We discuss drawbacks of each method individually and consider crucial points for experimental designs. The source code of our implementation is available under the terms of the GNU GPLv3 and can be downloaded from sourceforge (http://fqms.svn.sourceforge.net/svnroot/fqms). A tarball containing the data used for the evaluation is available on the FGCZ web server (http://fgcz-data.uzh.ch/public/T3PQ.tgz).     

Beyond the Venn diagram: the hunt for a core microbiome

Discovering a core microbiome is important for understanding the stable, consistent components across complex microbial assemblages. A core is typically defined as the suite of members shared among microbial consortia from similar habitats, and is represented by the overlapping areas of circles in Venn diagrams, in which each circle contains the membership of the sample or habitats being compared. Ecological insight into core microbiomes can be enriched by 'omics approaches that assess gene expression, thereby extending the concept of the core beyond taxonomically defined membership to community function and behaviour. Parameters defined by traditional ecology theory, such as composition, phylogeny, persistence and connectivity, will also create a more complex portrait of the core microbiome and advance understanding of the role of key microorganisms and functions within and across ecosystems.     

Comparison of Sequencing Based CNV Discovery Methods Using Monozygotic Twin Quartets

Background

The advent of high throughput sequencing methods breeds an important amount of technical challenges. Among those is the one raised by the discovery of copy-number variations (CNVs) using whole-genome sequencing data. CNVs are genomic structural variations defined as a variation in the number of copies of a large genomic fragment, usually more than one kilobase. Here, we aim to compare different CNV calling methods in order to assess their ability to consistently identify CNVs by comparison of the calls in 9 quartets of identical twin pairs. The use of monozygotic twins provides a means of estimating the error rate of each algorithm by observing CNVs that are inconsistently called when considering the rules of Mendelian inheritance and the assumption of an identical genome between twins. The similarity between the calls from the different tools and the advantage of combining call sets were also considered.

Results

ERDS and CNVnator obtained the best performance when considering the inherited CNV rate with a mean of 0.74 and 0.70, respectively. Venn diagrams were generated to show the agreement between the different algorithms, before and after filtering out familial inconsistencies. This filtering revealed a high number of false positives for CNVer and Breakdancer. A low overall agreement between the methods suggested a high complementarity of the different tools when calling CNVs. The breakpoint sensitivity analysis indicated that CNVnator and ERDS achieved better resolution of CNV borders than the other tools. The highest inherited CNV rate was achieved through the intersection of these two tools (81%).

Conclusions

This study showed that ERDS and CNVnator provide good performance on whole genome sequencing data with respect to CNV consistency across families, CNV breakpoint resolution and CNV call specificity. The intersection of the calls from the two tools would be valuable for CNV genotyping pipelines.     

Microbial communities in an anaerobic dynamic membrane bioreactor (AnDMBR) for municipal wastewater treatment: Comparison of bulk sludge and cake layer

454 high-throughput pyrosequencing was employed to investigate microbial communities in bulk sludge (BS) and cake layer (CL) in an anaerobic dynamic membrane bioreactor (AnDMBR). Pyrosequencing produced 7402 and 7026 high-quality V1–V3 tags of the 16S rRNA-gene for the BS and CL samples, and the number of total OTUs estimated by Chao1 was 2906 (BS) and 2532 (CL) at a 3% distance. Phylogenetic spectrum and Venn diagrams revealed that the bacterial phyla in the two samples were nearly identical, and that the predominant microorganisms of them exhibited a high homology. Nevertheless, population distribution was different between them. Proteobacteria were the most dominant in the BS, while Bacteroidetes, Firmicutes and Spirochaetes were highly enriched in the CL, accounting for 57.6% of the total microbes. The main microbial groups in the CL were highly functionally organized. Bacteroides, Clostridia and Delta-proteobacteria were likely the pioneers for surface colonization on membranes in the AnDMBR.