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.
Highlights
As our knowledge of the inter-connected complexity of physiological, cellular and molecular functions expands, there is an ever increasing need for novel methods to study multiple datasets simultaneously
Application of the chronic minimal peroxide’ (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 to stimulate signaling activity in the SH-SY5Y cells, methylcholine chloride (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 extracellular signal-regulated kinase 1/2 (ERK1/2), as we have previously reported [14]
Summary
As our knowledge of the inter-connected complexity of physiological, cellular and molecular functions expands, there is an ever increasing need for novel methods to study multiple datasets simultaneously. Venn himself generated visualization platforms that facilitate simultaneous analysis of higher numbers of sets, by using additional successive ellipses that intersect with the primary circles. He gave a construction for Venn diagrams for any number of sets, where each successive curve delimiting a set is interleaved with previous curves, starting with the 3-circle diagram [1]. The Edwards Venn diagram was achieved by projecting the classical circular Venn diagram onto a sphere In this format, three sets are represented by taking three hemispheres at right angles to each other, while a fourth set can be represented by taking a curve similar to the seam on a tennis ball which undulates around the sphere equator. The resulting sets can be projected back to a flat plane, generating ‘cogwheel’ diagrams with increasing numbers of teeth
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
