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

2018 ◽  
Vol 16 (03) ◽  
pp. 1850001 ◽  
Author(s):  
A. Ranjitha Dhanasekaran ◽  
Katheleen J. Gardiner
Keyword(s):  
Brain Regions ◽  
Large Datasets ◽  
Ease Of Use ◽  
Statistical Features ◽  
Software Suite ◽  
Reverse Phase ◽  
High Throughput Technology ◽  
Phase Protein ◽  
Biological Discovery

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.

Nachweis von Aromatase-Expression im eutopen Endometrium mittels reverse-phase Protein Arraying bei Patientinnen mit Endometriose

2008 ◽  
Vol 68 (S 01) ◽  
Author(s):  
MM Wölfler ◽  
C Siehs ◽  
K Schwamborn ◽  
D Otten ◽  
R Knüchel-Clarke ◽  
...  
Keyword(s):  
Reverse Phase ◽  
Aromatase Expression ◽  
Phase Protein

Reconstruction of Protein Networks Using Reverse-Phase Protein Array Data

2016 ◽  
pp. 227-246
Author(s):  
Silvia von der Heyde ◽  
Johanna Sonntag ◽  
Frank Kramer ◽  
Christian Bender ◽  
Ulrike Korf ◽  
...  
Keyword(s):  
Protein Array ◽  
Protein Networks ◽  
Reverse Phase Protein Array ◽  
Reverse Phase ◽  
Array Data ◽  
Phase Protein

The Role of Satisfaction and Ease of Use on User Attitudes of E-Learning: Case Study MI Mumtaza

2020 ◽  
Author(s):  
Sururin ◽  
Munzier Suparta ◽  
Herlino Nanang ◽  
Amelia Zakiyyatun Nufus ◽  
Kamarusdiana ◽  
...  
Keyword(s):  
Ease Of Use ◽  
User Attitudes ◽  
E Learning

Pegylated, Steptavidin-Conjugated Quantum Dots Are Effective Detection Elements for Reverse-Phase Protein Microarrays

2005 ◽  
Vol 16 (3) ◽  
pp. 559-566 ◽  
Author(s):  
David Geho ◽  
Nicholas Lahar ◽  
Prem Gurnani ◽  
Michael Huebschman ◽  
Paul Herrmann ◽  
...  
Keyword(s):  
Quantum Dots ◽  
Protein Microarrays ◽  
Reverse Phase ◽  
Phase Protein

Subtyping of breast cancer using reverse phase protein arrays

2014 ◽  
Vol 11 (6) ◽  
pp. 757-770 ◽  
Author(s):  
Johanna Sonntag ◽  
Kerstin Schlüter ◽  
Stephan Bernhardt ◽  
Ulrike Korf
Keyword(s):  
Breast Cancer ◽  
Reverse Phase ◽  
Protein Arrays ◽  
Phase Protein

scholarly journals NormaCurve: A SuperCurve-Based Method That Simultaneously Quantifies and Normalizes Reverse Phase Protein Array Data

PLoS ONE ◽  
2012 ◽  
Vol 7 (6) ◽  
pp. e38686 ◽  
Author(s):  
Sylvie Troncale ◽  
Aurélie Barbet ◽  
Lamine Coulibaly ◽  
Emilie Henry ◽  
Beilei He ◽  
...  
Keyword(s):  
Protein Array ◽  
Reverse Phase Protein Array ◽  
Reverse Phase ◽  
Array Data ◽  
Phase Protein

Reverse Phase Protein Microarrays for Monitoring Biological Responses

2007 ◽  
pp. 321-336 ◽  
Author(s):  
Virginia Espina ◽  
Julia D. Wulfkuhle ◽  
Valerie S. Calvert ◽  
Emanuel F. Petricoin ◽  
Lance A. Liotta
Keyword(s):  
Protein Microarrays ◽  
Reverse Phase ◽  
Biological Responses ◽  
Phase Protein

scholarly journals Analysis of Reverse Phase Protein Array Data: From Experimental Design towards Targeted Biomarker Discovery

Microarrays ◽  
2015 ◽  
Vol 4 (4) ◽  
pp. 520-539 ◽  
Author(s):  
Astrid Wachter ◽  
Stephan Bernhardt ◽  
Tim Beissbarth ◽  
Ulrike Korf
Keyword(s):  
Experimental Design ◽  
Biomarker Discovery ◽  
Protein Array ◽  
Reverse Phase Protein Array ◽  
Reverse Phase ◽  
Array Data ◽  
Phase Protein

Selecting a Pesticide Fate Model at the Watershed Scale Using a Multi-criteria Analysis

2006 ◽  
Vol 41 (3) ◽  
pp. 283-295 ◽  
Author(s):  
Renaud Quilbé ◽  
Alain N. Rousseau ◽  
Pierre Lafrance ◽  
Jacinthe Leclerc ◽  
Mohamed Amrani
Keyword(s):  
Best Management Practices ◽  
Management Practices ◽  
Ease Of Use ◽  
Watershed Scale ◽  
Water Quality Standards ◽  
Best Management ◽  
Multi Criteria Analysis ◽  
Selection Framework ◽  
Selection Of

Abstract Numerous models have been developed over the last decades to simulate the fate of pesticides at the watershed scale. Based on a literature review, we inventoried thirty-six models categorized as management, research, screening or multimedia models, each of them having specific strengths and weaknesses. Given this large number of models, it may be difficult for potential users (stakeholders or scientists) to find the most suited one with respect to their needs. To help in this process, this paper proposes a pragmatic approach based on a multi-criteria analysis. Selection criteria are defined following the user's needs and classified in five classes: modelling characteristics, output variables, model applicability, possibilities to simulate best management practices (BMPs) and ease of use. The relative importance of each criterion is quantified by a weight and the total score of a model is calculated by adding the resulting weights of satisfied criteria. This selection framework is illustrated with a case study that consists in selecting a model to develop water quality standards at the watershed scale with respect to the implementation of BMPs. This resulted in the selection of three models: BASINS, SWAT and GIBSI.

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