ArticleBioinformatics (Oxford, England)2022
RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 19 citations in OpenAlex.
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- Non-cell-autonomous tumor promotion in DICER1 cancer predisposition.Developmental cell · 2026Article
- Efferocytosis related KCTD12 is a clinico-immune target in lung adenocarcinoma.Frontiers in oncology · 2026Article
- Dietary Fat Content Influences PanIN Progression and Pancreatic Cancer Development in Mice.bioRxiv : the preprint server for biology · 2025Article
- Galectin-9 regulates dendritic cell polarity and uropod contraction by modulating RhoA activity.The Journal of cell biology · 2025Article
- An allele-agnostic mutant-KRAS inhibitor suppresses tumor maintenance signals and reprograms tumor immunity in pancreatic cancer.Science translational medicine · 2025Article
- Suppressing proteasome activity enhances sensitivity to actinomycin D in diffuse anaplastic Wilms tumor.Cell reports. Medicine · 2025Article
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- Vertical inhibition of p110α/AKT and N-cadherin enhances treatment efficacy in PIK3CA-aberrated ovarian cancer cells.Molecular oncology · 2025Article
- Caveolin-1 regulates context-dependent signaling and survival in Ewing sarcoma.bioRxiv : the preprint server for biology · 2025Article
- Actinomycin D and bortezomib disrupt protein homeostasis in Wilms tumor.bioRxiv : the preprint server for biology · 2024Article
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- Article
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Corrections and comments
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Authors and funding
12 authors at 2 institutions in 1 country.
Funding
Abstract
summaryReverse-Phase Protein Array (RPPA) is a robust high-throughput, cost-effective platform for quantitatively measuring proteins in biological specimens. However, converting raw RPPA data into normalized, analysis-ready data remains a challenging task. Here, we present the RPPA SPACE (RPPA Superposition Analysis and Concentration Evaluation) R package, a substantially improved successor to SuperCurve, to meet that challenge. SuperCurve has been used to normalize over 170 000 samples to date. RPPA SPACE allows exclusion of poor-quality samples from the normalization process to improve the quality of the remaining samples. It also features a novel quality-control metric, 'noise', that estimates the level of random errors present in each RPPA slide. The noise metric can help to determine the quality and reliability of the data. In addition, RPPA SPACE has simpler input requirements and is more flexible than SuperCurve, it is much faster with greatly improved error reporting. AVAILABILITY AND IMPLEMENTATION: The standalone RPPA SPACE R package, tutorials and sample data are available via https://rppa.space/, CRAN (https://cran.r-project.org/web/packages/RPPASPACE/index.html) and GitHub (https://github.com/MD-Anderson-Bioinformatics/RPPASPACE). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.