RPPApipe: a pipeline for the analysis of reverse-phase protein array data

Johannes Eichner; Yvonne Heubach; Manuel Ruff; Hella Kohlhof; Stefan Strobl; Barbara Mayer; Michael Pawlak; Markus F Templin; Andreas Zell

doi:10.1016/j.biosystems.2014.06.009

RPPApipe: a pipeline for the analysis of reverse-phase protein array data

Biosystems. 2014 Aug:122:19-24. doi: 10.1016/j.biosystems.2014.06.009. Epub 2014 Jun 18.

Authors

Johannes Eichner¹, Yvonne Heubach², Manuel Ruff³, Hella Kohlhof⁴, Stefan Strobl⁴, Barbara Mayer⁵, Michael Pawlak², Markus F Templin², Andreas Zell³

Affiliations

¹ Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72076, Germany. Electronic address: johannes.eichner@uni-tuebingen.de.
² Natural and Medical Sciences Institute at the University of Tuebingen (NMI), Reutlingen 72770, Germany.
³ Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72076, Germany.
⁴ 4SC AG, Planegg-Martinsried 82152, Germany.
⁵ SpheroTec GmbH, Planegg-Martinsried 82152, Germany.

PMID: 24951946
DOI: 10.1016/j.biosystems.2014.06.009

Abstract

Background and scope: Today, web-based data analysis pipelines exist for a wide variety of microarray platforms, such as ordinary gene-centered arrays, exon arrays and SNP arrays. However, most of the available software tools provide only limited support for reverse-phase protein arrays (RPPA), as relevant inherent properties of the corresponding datasets are not taken into account. Thus, we developed the web-based data analysis pipeline RPPApipe, which was specifically tailored to suit the characteristics of the RPPA platform and encompasses various tools for data preprocessing, statistical analysis, clustering and pathway analysis.

Implementation and performance: All tools which are part of the RPPApipe software were implemented using R/Bioconductor. The software was embedded into our web-based ZBIT Bioinformatics Toolbox which is a customized instance of the Galaxy platform.

Availability: RPPApipe is freely available under GNU Public License from http://webservices.cs.uni-tuebingen.de. A full documentation of the tool can be found on the corresponding website http://www.cogsys.cs.uni-tuebingen.de/software/RPPApipe.

Keywords: Clustering; Pathway analysis; Reverse-phase protein arrays; Statistical analysis; Visualization; Web application.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods*
Data Interpretation, Statistical*
Internet
Protein Array Analysis / methods*
Software*