Reverse phase protein array data analysis software tools
Reverse phase protein array (RPPA) technology, first described in 2001, allows simultaneous measurement of numerous glycosylated, phosphorylated, cleaved, or total cellular proteins from complex mixtures in many samples at once. RPPA is considerably faster than conventional techniques such as mass spectrometry, western blotting, 2-D PAGE.
Allows exploration of global patterns of reverse phase protein arrays (RPPA) datasets. TCPA provides expression levels of key cancer proteins from approximately 10 000 samples of both patient tumors and cancer cell lines. It can be used as a resource for assisting users in building testable hypotheses, validating findings of interest, and more globally as a tool for simplifying the development of novel cancer therapies.
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.
A classifier for quality control of RPPA experiments using a generalized linear model and logistic function. The outcome of the classifier, ranging from 0 to 1, is defined as the probability that a slide is of good quality. The classifier is implemented in the “SuperCurve” R package.
A comprehensive and user-friendly web application bridging the gap between spotting and array analysis by conveniently keeping track of sample information. Data processing includes correction of staining bias, estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation. Established analysis methods have been integrated with MIRACLE, offering experimental scientists an end-to-end solution for sample management and for carrying out data analysis. In addition, experienced users have the possibility to export data to R for more complex analyses.
Allows to simultaneously quantify and normalize Reverse Phase Protein Arrays (RPPAs). NormaCurve is a normalization model that considers the two control arrays ctrl and sypro, as well as the two spatial effects Row and Column. The model, validated by cross-validation, allows the correction of spatial effects and corrects for differences in total amount of spotted proteins. It does not require a minimum amount of antibodies to be powerful and it is not affected by a bias in the chosen antibodies.
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