Reverse phase protein array (rppa)

Processes within a cell are mainly performed by proteins. Special copies of a gene, called messenger RNAs (mRNAs), are produced and transported to the cells protein synthesis machinery to produce the corresponding protein. The more mRNA molecules of a gene cause the more of its corresponding protein is produced. However, this is not always a linear relationship. Presence or absence of some molecules (including other proteins) can inhibit or enhance the production of a protein.

High-throughput technologies such as micro-arrays and RNA/DNA sequencing technologies measure the level of mRNA as a surrogate marker for protein level. There are a few highthroughput technologies that allow direct measurement of the protein levels. The reverse phase protein array (RPPA) is one such technology. To perform RPPA, cell/tissue lysate of interest is printed as small dots (droplets) of the same size on surface of a special plate. Each dot on the plate is then stained with fluorochrome conjugated antibodies against one specific protein. The plate is then washed and scanned to detect the fluorescence. Since most antibodies bind to multiple proteins due to non-specific binding, the requirement for antibodies which only detect a single protein in one of the limitation of RPPA.

In this workflow, RPPA dataset from TCGA consortium is clustered using R hierarchical clustering and K-means clustering from ‘stats’ package.

RPPA workflow

Packages and Dependencies

There is ony 1 package used in this workflow, which has no dependencies.

Used packages:

• CORE: stats

Data

• RPPA data: http://tcga-data.nci.nih.gov/docs/publications/TCGApancan_2014/RPPA_input.csv

License

• Copyright (c) 2015 Ieuan Clay based on code from genbench
• Copyright (c) 2015-2016 BeDataDriven B.V. License: GPL version 2 or higher