Literature DB >> 20634205

RPPanalyzer: Analysis of reverse-phase protein array data.

Heiko A Mannsperger1, Stephan Gade, Frauke Henjes, Tim Beissbarth, Ulrike Korf.   

Abstract

SUMMARY: RPPanalyzer is a statistical tool developed to read reverse-phase protein array data, to perform the basic data analysis and to visualize the resulting biological information. The R-package provides different functions to compare protein expression levels of different samples and to normalize the data. Implemented plotting functions permit a quality control by monitoring data distribution and signal validity. Finally, the data can be visualized in heatmaps, boxplots, time course plots and correlation plots. RPPanalyzer is a flexible tool and tolerates a huge variety of different experimental designs. AVAILABILITY: The RPPAanalyzer is open source and freely available as an R-Package on the CRAN platform http://cran.r-project.org/.

Mesh：

Year:  2010        PMID： 20634205     DOI： 10.1093/bioinformatics/btq347

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  25 in total

1.  Reno: regularized non-parametric analysis of protein lysate array data.

Authors:  Bin Li; Feng Liang; Jianhua Hu; And Xuming He
Journal:  Bioinformatics       Date:  2012-03-30       Impact factor: 6.937

2.  Profiling Humoral Immune Responses to Clostridium difficile-Specific Antigens by Protein Microarray Analysis.

Authors:  Ola H Negm; Mohamed R Hamed; Elizabeth M Dilnot; Clifford C Shone; Izabela Marszalowska; Mark Lynch; Christine E Loscher; Laura J Edwards; Patrick J Tighe; Mark H Wilcox; Tanya M Monaghan
Journal:  Clin Vaccine Immunol       Date:  2015-07-15

3.  A Protein Microarray Assay for Serological Determination of Antigen-specific Antibody Responses Following Clostridium difficile Infection.

Authors:  Ola H Negm; Mohamed Hamed; Tanya M Monaghan
Journal:  J Vis Exp       Date:  2018-06-15       Impact factor: 1.355

4.  Protein network construction using reverse phase protein array data.

Authors:  Rency S Varghese; Yiming Zuo; Yi Zhao; Yong-Wei Zhang; Sandra A Jablonski; Mariaelena Pierobon; Emanuel F Petricoin; Habtom W Ressom; Louis M Weiner
Journal:  Methods       Date:  2017-06-24       Impact factor: 3.608

5.  Patients with tumour necrosis factor (TNF) receptor-associated periodic syndrome (TRAPS) are hypersensitive to Toll-like receptor 9 stimulation.

Authors:  O H Negm; S Singh; W Abduljabbar; M R Hamed; P Radford; E M McDermott; E Drewe; L Fairclough; I Todd; P J Tighe
Journal:  Clin Exp Immunol       Date:  2019-05-22       Impact factor: 4.330

6.  limma powers differential expression analyses for RNA-sequencing and microarray studies.

Authors:  Matthew E Ritchie; Belinda Phipson; Di Wu; Yifang Hu; Charity W Law; Wei Shi; Gordon K Smyth
Journal:  Nucleic Acids Res       Date:  2015-01-20       Impact factor: 16.971

Review 7.  Using reverse-phase protein arrays as pharmacodynamic assays for functional proteomics, biomarker discovery, and drug development in cancer.

Authors:  Yiling Lu; Shiyun Ling; Apurva M Hegde; Lauren A Byers; Kevin Coombes; Gordon B Mills; Rehan Akbani
Journal:  Semin Oncol       Date:  2016-06-15       Impact factor: 4.929

8.  Realizing the promise of reverse phase protein arrays for clinical, translational, and basic research: a workshop report: the RPPA (Reverse Phase Protein Array) society.

Authors:  Rehan Akbani; Karl-Friedrich Becker; Neil Carragher; Ted Goldstein; Leanne de Koning; Ulrike Korf; Lance Liotta; Gordon B Mills; Satoshi S Nishizuka; Michael Pawlak; Emanuel F Petricoin; Harvey B Pollard; Bryan Serrels; Jingchun Zhu
Journal:  Mol Cell Proteomics       Date:  2014-04-28       Impact factor: 5.911

9.  Triplex DNA-binding proteins are associated with clinical outcomes revealed by proteomic measurements in patients with colorectal cancer.

Authors:  Laura D Nelson; Christian Bender; Heiko Mannsperger; Daniel Buergy; Patryk Kambakamba; Giridhar Mudduluru; Ulrike Korf; Dennis Hughes; Michael W Van Dyke; Heike Allgayer
Journal:  Mol Cancer       Date:  2012-06-08       Impact factor: 27.401

10.  Sequential stopping for high-throughput experiments.

Authors:  David Rossell; Peter Müller
Journal:  Biostatistics       Date:  2012-08-20       Impact factor: 5.899
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