A pipeline for the analysis of reverse-phase protein array data.

Johannes Eichner1, Manuel Ruff1, Yvonne Heubach2, Markus Templin2, Michael Pawlak2, Andreas Zell1

1Center for Bioinformatics Tübingen (ZBIT), Germany
2Natural and Medical Sciences Institute at the University of Tübingen (NMI), Reutlingen, Germany

Short description:
RPPApipe is an easy-to-use, web-based analysis pipeline for the normalization, annotation, statistical analysis, visualization, clustering and pathway analysis of Reverse-Phase Protein Array (RPPA) datasets. In contrast to ordinary microarray data analysis pipelines, the tool offers specifically designed features for RPPA data analysis and visualization. One of the key aspects is the consideration of post-translational modifications (e.g., phosphorylation, acetylation, etc.), which may have a significant impact on protein function and activity. Besides ordinary differential expression analysis, differential protein modification can be detected and visualized in specially adapted volcano plots. Furthermore, since RPPAs are typically applied to profile protein expresson in diverse biological samples in a dose- and time-dependent manner, we designed a special clustering approach which results in a condensed heatmap visualization simplifying further biological interpretation. In addition to the built-in features for pathway analysis, the processed data can be easily exported to our InCroMAP software, which facilitates the interactive visualization of phosphoproteomics data in the context of canonical signaling networks. All data processing steps can be easily automated either by using predefined workflows or by constructing a custom-built analysis pipeline in a convenient web-based workflow editor. The uploaded datasets, constructed workflows, and generated results can be saved in a personal history.

RPPApipe is available as an online tool which is part of our Bioinformatics Toolbox:

RPPApipe webtool

A full documentation of the software including a short tutorial, diverse example datasets and detailed descriptions of each tool can be found here.


GPL version 3 RPPApipe is subject to the GNU General Public License 3.0. See the License section for a more detailed description of the terms of use of this software.


Documentation: A complete documentation is now available.   -   (eichner - 2013-10-30 11:03)
Online Tool: The online tool RPPApipe is now available via our Bioinformatics Toolbox.   -   (eichner - 2013-10-30 13:19)


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