ArticlePloS one2014
Spatial normalization of reverse phase protein array data.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Establishment and characterization of patient-derived xenograft of a rare pediatric anaplastic pleomorphic xanthoastrocytoma (PXA) bearing a CDC42SE2-BRAF fusion.Scientific reports · 2023Article
- Article
- RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data.Bioinformatics (Oxford, England) · 2022Article
- Blood-Based Biomarkers of Repetitive, Subconcussive Blast Overpressure Exposure in the Training Environment: A Pilot Study.Neurotrauma reports · 2022Article
- Reverse phase protein arrays in acute leukemia: investigative and methodological challenges.Expert review of proteomics · 2021Review
- Integrative analysis of multi-platform reverse-phase protein array data for the pharmacodynamic assessment of response to targeted therapies.Scientific reports · 2020Article
- Probe-target hybridization depends on spatial uniformity of initial concentration condition across large-format chips.Scientific reports · 2020Article
- Nonlinear mixed effects dose response modeling in high throughput drug screens: application to melanoma cell line analysis.Oncotarget · 2018Article
- Proteomic Screening and Lasso Regression Reveal Differential Signaling in Insulin and Insulin-like Growth Factor I (IGF1) Pathways.Molecular & cellular proteomics : MCP · 2016Article
- Procollagen markers in microdialysate can predict patient outcome after Achilles tendon rupture.BMJ open sport & exercise medicine · 2016Article
- Analysis of Reverse Phase Protein Array Data: From Experimental Design towards Targeted Biomarker Discovery.Microarrays (Basel, Switzerland) · 2015Review
- Reverse Phase Protein Arrays-Quantitative Assessment of Multiple Biomarkers in Biopsies for Clinical Use.Microarrays (Basel, Switzerland) · 2015Review
- Drug synergy screen and network modeling in dedifferentiated liposarcoma identifies CDK4 and IGF1R as synergistic drug targets.Science signaling · 2013Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Reverse phase protein arrays (RPPA) are an efficient, high-throughput, cost-effective method for the quantification of specific proteins in complex biological samples. The quality of RPPA data may be affected by various sources of error. One of these, spatial variation, is caused by uneven exposure of different parts of an RPPA slide to the reagents used in protein detection. We present a method for the determination and correction of systematic spatial variation in RPPA slides using positive control spots printed on each slide. The method uses a simple bi-linear interpolation technique to obtain a surface representing the spatial variation occurring across the dimensions of a slide. This surface is used to calculate correction factors that can normalize the relative protein concentrations of the samples on each slide. The adoption of the method results in increased agreement between technical and biological replicates of various tumor and cell-line derived samples. Further, in data from a study of the melanoma cell-line SKMEL-133, several slides that had previously been rejected because they had a coefficient of variation (CV) greater than 15%, are rescued by reduction of CV below this threshold in each case. The method is implemented in the R statistical programing language. It is compatible with MicroVigene and SuperCurve, packages commonly used in RPPA data analysis. The method is made available, along with suggestions for implementation, at http://bitbucket.org/rppa_preprocess/rppa_preprocess/src.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.