RPPApipe: a Pipeline for the Analysis of Reverse-phase Protein Array Data
Overview
Authors
Affiliations
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.
Penile Cancer-Derived Cells Molecularly Characterized as Models to Guide Targeted Therapies.
Kuasne H, Matos do Canto L, Aagaard M, Munoz J, De Jamblinne C, Marchi F Cells. 2021; 10(4).
PMID: 33917394 PMC: 8067406. DOI: 10.3390/cells10040814.
Protein network construction using reverse phase protein array data.
Varghese R, Zuo Y, Zhao Y, Zhang Y, Jablonski S, Pierobon M Methods. 2017; 124:89-99.
PMID: 28651964 PMC: 5603262. DOI: 10.1016/j.ymeth.2017.06.017.
Wachter A, Bernhardt S, Beissbarth T, Korf U Microarrays (Basel). 2016; 4(4):520-39.
PMID: 27600238 PMC: 4996411. DOI: 10.3390/microarrays4040520.
ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.
Romer M, Eichner J, Drager A, Wrzodek C, Wrzodek F, Zell A PLoS One. 2016; 11(2):e0149263.
PMID: 26882475 PMC: 4801062. DOI: 10.1371/journal.pone.0149263.
Reverse phase protein arrays: mapping the path towards personalized medicine.
Gallagher R, Espina V Mol Diagn Ther. 2014; 18(6):619-30.
PMID: 25358623 PMC: 4732707. DOI: 10.1007/s40291-014-0122-3.