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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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Chronic minimal peroxide-mediated alteration of protein expression and ligand responses.(A) Representative western immunoblot (IB) analysis of control (PBS-vehicle treated) or CMP treatment (7 days, 10 nM hydrogen peroxide treatment) effects upon cellular expression of lamin A (LMNA), G protein-coupled receptor kinase interacting ArfGAP 2 (GIT2), calreticulin (CALR) and calmodulin (CALM1). Quantification of CMP-mediated expression changes of LMNA (B), GIT2 (C), CALM1 (D) and CALR (E). Quantification was achieved as follows: western blot relative absorbance units (x1000) minus background absorbance subtraction per square pixel: ((AU-B)/px2). Quantification was performed using ImageQuant 5.2 and statistical analysis was performed on three independent experiments using GraphPad Prism version 5.02 with a Student’s t-test (p<0.05, *; p<0.01, **; p<0.001, ***). Data is represented as mean ± standard error of mean (SEM). (F) Log dose-response curves for acetyl-β-methycholine (MeCh)-mediated ERK1/2 activation in control (black circles) or CMP-treated (white square) cells. (G) Response-normalized MeCh ERK1/2 log dose-response curves. The maximal response for MeCh in each cellular context (control versus CMP) was considered to be 100% in each circumstance. Each experimental point on the curves (fitted using sigmoidal dose-response functions in GraphPad Prism) represents the mean ± SEM of three independent experiments.
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pone-0036911-g001: Chronic minimal peroxide-mediated alteration of protein expression and ligand responses.(A) Representative western immunoblot (IB) analysis of control (PBS-vehicle treated) or CMP treatment (7 days, 10 nM hydrogen peroxide treatment) effects upon cellular expression of lamin A (LMNA), G protein-coupled receptor kinase interacting ArfGAP 2 (GIT2), calreticulin (CALR) and calmodulin (CALM1). Quantification of CMP-mediated expression changes of LMNA (B), GIT2 (C), CALM1 (D) and CALR (E). Quantification was achieved as follows: western blot relative absorbance units (x1000) minus background absorbance subtraction per square pixel: ((AU-B)/px2). Quantification was performed using ImageQuant 5.2 and statistical analysis was performed on three independent experiments using GraphPad Prism version 5.02 with a Student’s t-test (p<0.05, *; p<0.01, **; p<0.001, ***). Data is represented as mean ± standard error of mean (SEM). (F) Log dose-response curves for acetyl-β-methycholine (MeCh)-mediated ERK1/2 activation in control (black circles) or CMP-treated (white square) cells. (G) Response-normalized MeCh ERK1/2 log dose-response curves. The maximal response for MeCh in each cellular context (control versus CMP) was considered to be 100% in each circumstance. Each experimental point on the curves (fitted using sigmoidal dose-response functions in GraphPad Prism) represents the mean ± SEM of three independent experiments.

Mentions: The proteomic effects, in human SH-SY5Y neural cells, of our previously-described chronic minimal peroxide (CMP) protocol was assessed, using a panel of divergently CMP-regulated proteins we had previously identified as specific markers of this modified cellular state [14] (Figure 1). Application of the CMP protocol to SH-SY5Y cells resulted in a significant upregulation of both lamin (LAMN) and GIT2 (G protein-coupled receptor kinase interacting ArfGAP 2: Figure 1A, B-C) and simultaneous, significant downregulation of calmodulin (CALM) and calreticulin (CALR) (Figure 1A, D-E). To assess the ability of the stable acetylcholine analog (acetyl-β-methylcholine: MeCh) to stimulate signaling activity in the SH-SY5Y cells, MeCh-mediated extracellular signal-regulated kinase (ERK1/2) activation was assessed. In both control-state and CMP-treated SH-SY5Y cells MeCh application resulted in a dose-dependent increase in the activity status of ERK1/2, as we have previously reported [14]. The basal level of non-phosphorylated as well as phosphorylated ERK1/2 was not significantly altered by the CMP protocol. From log dose-response analysis, it was apparent that the alteration in cellular context induced by CMP, caused an increase in the maximal response (Rmax) to MeCh (Figure 1F). ERK1/2 activation responses to each of the doses of MeCh tested (in both control- and CMP-state cells) were effectively blocked by the pre-exposure of the SH-SY5Y cells to the selective muscarinic G protein-coupled receptor antagonist pirenzipine (10 µM, 30 minutes incubation prior to MeCh exposure). In addition, no significant alteration of plasma membrane muscarinic receptor expression was noted between control and CMP conditions (Figure S1: [14]).


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)

Chronic minimal peroxide-mediated alteration of protein expression and ligand responses.(A) Representative western immunoblot (IB) analysis of control (PBS-vehicle treated) or CMP treatment (7 days, 10 nM hydrogen peroxide treatment) effects upon cellular expression of lamin A (LMNA), G protein-coupled receptor kinase interacting ArfGAP 2 (GIT2), calreticulin (CALR) and calmodulin (CALM1). Quantification of CMP-mediated expression changes of LMNA (B), GIT2 (C), CALM1 (D) and CALR (E). Quantification was achieved as follows: western blot relative absorbance units (x1000) minus background absorbance subtraction per square pixel: ((AU-B)/px2). Quantification was performed using ImageQuant 5.2 and statistical analysis was performed on three independent experiments using GraphPad Prism version 5.02 with a Student’s t-test (p<0.05, *; p<0.01, **; p<0.001, ***). Data is represented as mean ± standard error of mean (SEM). (F) Log dose-response curves for acetyl-β-methycholine (MeCh)-mediated ERK1/2 activation in control (black circles) or CMP-treated (white square) cells. (G) Response-normalized MeCh ERK1/2 log dose-response curves. The maximal response for MeCh in each cellular context (control versus CMP) was considered to be 100% in each circumstance. Each experimental point on the curves (fitted using sigmoidal dose-response functions in GraphPad Prism) represents the mean ± SEM of three independent experiments.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3351456&req=5

pone-0036911-g001: Chronic minimal peroxide-mediated alteration of protein expression and ligand responses.(A) Representative western immunoblot (IB) analysis of control (PBS-vehicle treated) or CMP treatment (7 days, 10 nM hydrogen peroxide treatment) effects upon cellular expression of lamin A (LMNA), G protein-coupled receptor kinase interacting ArfGAP 2 (GIT2), calreticulin (CALR) and calmodulin (CALM1). Quantification of CMP-mediated expression changes of LMNA (B), GIT2 (C), CALM1 (D) and CALR (E). Quantification was achieved as follows: western blot relative absorbance units (x1000) minus background absorbance subtraction per square pixel: ((AU-B)/px2). Quantification was performed using ImageQuant 5.2 and statistical analysis was performed on three independent experiments using GraphPad Prism version 5.02 with a Student’s t-test (p<0.05, *; p<0.01, **; p<0.001, ***). Data is represented as mean ± standard error of mean (SEM). (F) Log dose-response curves for acetyl-β-methycholine (MeCh)-mediated ERK1/2 activation in control (black circles) or CMP-treated (white square) cells. (G) Response-normalized MeCh ERK1/2 log dose-response curves. The maximal response for MeCh in each cellular context (control versus CMP) was considered to be 100% in each circumstance. Each experimental point on the curves (fitted using sigmoidal dose-response functions in GraphPad Prism) represents the mean ± SEM of three independent experiments.
Mentions: The proteomic effects, in human SH-SY5Y neural cells, of our previously-described chronic minimal peroxide (CMP) protocol was assessed, using a panel of divergently CMP-regulated proteins we had previously identified as specific markers of this modified cellular state [14] (Figure 1). Application of the CMP protocol to SH-SY5Y cells resulted in a significant upregulation of both lamin (LAMN) and GIT2 (G protein-coupled receptor kinase interacting ArfGAP 2: Figure 1A, B-C) and simultaneous, significant downregulation of calmodulin (CALM) and calreticulin (CALR) (Figure 1A, D-E). To assess the ability of the stable acetylcholine analog (acetyl-β-methylcholine: MeCh) to stimulate signaling activity in the SH-SY5Y cells, MeCh-mediated extracellular signal-regulated kinase (ERK1/2) activation was assessed. In both control-state and CMP-treated SH-SY5Y cells MeCh application resulted in a dose-dependent increase in the activity status of ERK1/2, as we have previously reported [14]. The basal level of non-phosphorylated as well as phosphorylated ERK1/2 was not significantly altered by the CMP protocol. From log dose-response analysis, it was apparent that the alteration in cellular context induced by CMP, caused an increase in the maximal response (Rmax) to MeCh (Figure 1F). ERK1/2 activation responses to each of the doses of MeCh tested (in both control- and CMP-state cells) were effectively blocked by the pre-exposure of the SH-SY5Y cells to the selective muscarinic G protein-coupled receptor antagonist pirenzipine (10 µM, 30 minutes incubation prior to MeCh exposure). In addition, no significant alteration of plasma membrane muscarinic receptor expression was noted between control and CMP conditions (Figure S1: [14]).

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