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

Martin B, Chadwick W, Yi T, Park SS, Lu D, Ni B, Gadkaree S, Farhang K, Becker KG, Maudsley S - PLoS ONE (2012)

Bottom Line: 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.Applied to complex pharmacological datasets, VENNTURE's improved features and ease of analysis are much improved over currently available Venn diagram programs.This study highlights the potential for such a program in fields such as pharmacology, genomics, and bioinformatics.

View Article: PubMed Central - PubMed

Affiliation: Metabolism Unit, Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America.

ABSTRACT
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.

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Related in: MedlinePlus

Multiple set VENNTURE data input.(A) In addition to simplistic data (two set analysis) input into VENNTURE, the program is flexible in that it can accept up to 6 input sets. With increasing set input, from Excel™ files, is a concomitant elevation in diagram complexity along with the eventual dataset output in column format in an Excel™ spreadsheet. With increasing numbers of input sets VENNTURE automatically alters its Venn output and organizes the eventual column display in Excel™. (B) Basic flow-chart for use of VENNTURE in the experimental investigation of the log dose-response of MeCh-induced phosphoproteomic changes in multiple cellular contexts. VENNTURE data output can be used for diagram generation (PowerPoint™ output), direct inspection Venn intersection contents (direct roll-over reveal option) and output for mathematical calculation (Excel™).
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pone-0036911-g004: Multiple set VENNTURE data input.(A) In addition to simplistic data (two set analysis) input into VENNTURE, the program is flexible in that it can accept up to 6 input sets. With increasing set input, from Excel™ files, is a concomitant elevation in diagram complexity along with the eventual dataset output in column format in an Excel™ spreadsheet. With increasing numbers of input sets VENNTURE automatically alters its Venn output and organizes the eventual column display in Excel™. (B) Basic flow-chart for use of VENNTURE in the experimental investigation of the log dose-response of MeCh-induced phosphoproteomic changes in multiple cellular contexts. VENNTURE data output can be used for diagram generation (PowerPoint™ output), direct inspection Venn intersection contents (direct roll-over reveal option) and output for mathematical calculation (Excel™).

Mentions: Our novel software program, VENNTURE, is constructed to allow simple data (e.g. two to six datasets of any length) uploading from commonly used software (Excel™), facilitate various forms of dataset annotation display and allow simple exportation of results to commonly used data and visual analytical tools (Excel™, Powerpoint™) (Figure 3). Employing a classical Edwards ‘cogwheel’ approach, VENNTURE is able to accommodate between 2 and 6 individual datasets that generate an ever-increasing series of Excel™ spreadsheet data output, due to a rapid increase in Venn diagram intersection complexity (Figure 4A). For our primary application in this study, we have generated two groups (control or CMP) of six separate datasets of proteins displaying a ligand-mediated phosphorylated status which we then uploaded into VENNTURE. We then employed VENNTURE for spreadsheet analysis, visual analytical output and also for direct visual appreciation of protein identification in each intersection using VENNTURE’s ‘roll-over’ annotation option (Figure 4B).


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

Martin B, Chadwick W, Yi T, Park SS, Lu D, Ni B, Gadkaree S, Farhang K, Becker KG, Maudsley S - PLoS ONE (2012)

Multiple set VENNTURE data input.(A) In addition to simplistic data (two set analysis) input into VENNTURE, the program is flexible in that it can accept up to 6 input sets. With increasing set input, from Excel™ files, is a concomitant elevation in diagram complexity along with the eventual dataset output in column format in an Excel™ spreadsheet. With increasing numbers of input sets VENNTURE automatically alters its Venn output and organizes the eventual column display in Excel™. (B) Basic flow-chart for use of VENNTURE in the experimental investigation of the log dose-response of MeCh-induced phosphoproteomic changes in multiple cellular contexts. VENNTURE data output can be used for diagram generation (PowerPoint™ output), direct inspection Venn intersection contents (direct roll-over reveal option) and output for mathematical calculation (Excel™).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3351456&req=5

pone-0036911-g004: Multiple set VENNTURE data input.(A) In addition to simplistic data (two set analysis) input into VENNTURE, the program is flexible in that it can accept up to 6 input sets. With increasing set input, from Excel™ files, is a concomitant elevation in diagram complexity along with the eventual dataset output in column format in an Excel™ spreadsheet. With increasing numbers of input sets VENNTURE automatically alters its Venn output and organizes the eventual column display in Excel™. (B) Basic flow-chart for use of VENNTURE in the experimental investigation of the log dose-response of MeCh-induced phosphoproteomic changes in multiple cellular contexts. VENNTURE data output can be used for diagram generation (PowerPoint™ output), direct inspection Venn intersection contents (direct roll-over reveal option) and output for mathematical calculation (Excel™).
Mentions: Our novel software program, VENNTURE, is constructed to allow simple data (e.g. two to six datasets of any length) uploading from commonly used software (Excel™), facilitate various forms of dataset annotation display and allow simple exportation of results to commonly used data and visual analytical tools (Excel™, Powerpoint™) (Figure 3). Employing a classical Edwards ‘cogwheel’ approach, VENNTURE is able to accommodate between 2 and 6 individual datasets that generate an ever-increasing series of Excel™ spreadsheet data output, due to a rapid increase in Venn diagram intersection complexity (Figure 4A). For our primary application in this study, we have generated two groups (control or CMP) of six separate datasets of proteins displaying a ligand-mediated phosphorylated status which we then uploaded into VENNTURE. We then employed VENNTURE for spreadsheet analysis, visual analytical output and also for direct visual appreciation of protein identification in each intersection using VENNTURE’s ‘roll-over’ annotation option (Figure 4B).

Bottom Line: 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.Applied to complex pharmacological datasets, VENNTURE's improved features and ease of analysis are much improved over currently available Venn diagram programs.This study highlights the potential for such a program in fields such as pharmacology, genomics, and bioinformatics.

View Article: PubMed Central - PubMed

Affiliation: Metabolism Unit, Laboratory of Clinical Investigation, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, United States of America.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus