The 2-dimensional gel electrophoresis is an important method in molecular biology to investigate proteins.
This project "Virtual-2DE" generates a virtual 2-dimensional gel electrophoresis plot which depicts the pI-value (isoelectric point) and the molecular weight Mr of all human proteins available in protein databases. Each spot represents a protein within Mr/pI - coordinates. The spot size is a measure of protein abundance. The Mr/pI values can be set within ranges defined by interactive sliders. The project "Virtual-2DE" is documented and a resulting plot is given as an example.
The "Virtual-2DE" project is deployed on shinyapps
The "Virtual-2DE" project is Rstudio Cloud project
Key technical details:
The physical characteristics of human proteins (Ref: Wang, T. Tang, H (2017), PLoS ONE 12(5): e0176234) are extended by protein abundance available in the protein abundance database PaxDb.
The resulting data table (EXCEL) contains 17262 human proteins with pI, Mr and abundance values. These data are depicted as 2-dim. plot in Mr/pI coordinates whereas the spot size is a measure of protein abundance.
Creating a dashboard with sliders for Mr/pI-ranges and arbitrary spot size one is able to select boxes or lasso from the plotly-package to obtain more information about a protein if you copy the URL under the key column and paste it into a browser to access the UniProt protein database.
The project is documented, the usage is described and an example plot is given.