RPPAware: A software suite to preprocess, analyze and visualize reverse phase protein array data

Journal of Bioinformatics and Computational Biology
A Ranjitha Dhanasekaran, Katheleen J Gardiner

Abstract

Reverse Phase Protein Arrays (RPPA) is a high-throughput technology used to profile levels of protein expression. Handling the large datasets generated by RPPA can be facilitated by appropriate software tools. Here, we describe RPPAware, a free and intuitive software suite that was developed specifically for analysis and visualization of RPPA data. RPPAware is a portable tool that requires no installation and was built using Java. Many modules of the tool invoke R to utilize the statistical features. To demonstrate the utility of RPPAware, data generated from screening brain regions of a mouse model of Down syndrome with 62 antibodies were used as a case study. The ease of use and efficiency of RPPAware can accelerate data analysis to facilitate biological discovery. RPPAware 1.0 is freely available under GNU General Public License from the project website at http://downsyndrome.ucdenver.edu/iddrc/rppaware/home.htm along with a full documentation of the tool.

References

Nov 5, 2003·Proteomics·Virginia EspinaLance A Liotta
Sep 24, 2005·Science·Aideen O'DohertyElizabeth M C Fisher
Oct 6, 2005·Statistics in Medicine·Rema Raman, Donald Hedeker
Jun 30, 2007·Bioinformatics·Jianhua HuGordon B Mills
Nov 1, 2008·Nature Protocols·Brett SpurrierSatoshi Nishizuka
Apr 2, 2009·Bioinformatics·E Shannon NeeleyKeith A Baggerly
Jul 17, 2010·Bioinformatics·Heiko A MannspergerUlrike Korf
Jan 5, 2012·Journal of Proteome Research·Md Mahiuddin AhmedKatheleen J Gardiner
Jun 12, 2012·Neural Plasticity·Noemí RuedaCarmen Martínez-Cué
Oct 30, 2012·Gene·Claire SpellmanKatheleen J Gardiner
Jan 26, 2013·Human Molecular Genetics·Md Mahiuddin AhmedKatheleen J Gardiner
Sep 17, 2013·Nature Methods·Jun LiHan Liang
Nov 19, 2013·Current Opinion in Genetics & Development·Hannah CarterTrey Ideker
Jun 22, 2014·Bio Systems·Johannes EichnerAndreas Zell
Jan 18, 2015·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Vianey Gonzalez-VillasanaGabriel Lopez-Berestein
May 28, 2015·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Grant D StewartThomas Powles
Jul 16, 2015·Pigment Cell & Melanoma Research·Ha Linh VuAndrew E Aplin

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Citations

Jan 23, 2019·BMC Bioinformatics·Christine P'ngPaul C Boutros

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