ArticleBioinformatics (Oxford, England)2009
Variable slope normalization of reverse phase protein arrays.
Article in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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Who cites it
58 citing papers in PubMed.
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- Carbonic anhydrase 9 expression increases with vascular endothelial growth factor-targeted therapy and is predictive of outcome in metastatic clear cell renal cancer.European urology · 2014Trial
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- Valosin-containing protein (VCP/p97) is prognostically unfavorable in pediatric AML, and negatively correlates with unfolded protein response proteins IRE1 and GRP78: A report from the Children's Oncology Group.Proteomics. Clinical applications · 2023Article
- Clinical relevance of proteomic profiling inHaematologica · 2022Article
- Tissue-Specific Downregulation of Fatty Acid Synthase Suppresses Intestinal Adenoma Formation via Coordinated Reprograming of Transcriptome and Metabolism in the Mouse Model of Apc-Driven Colorectal Cancer.International journal of molecular sciences · 2022Article
- The metabolic enzyme hexokinase 2 localizes to the nucleus in AML and normal haematopoietic stem and progenitor cells to maintain stemness.Nature cell biology · 2022Article
- Adaptation and Changes in Actin Dynamics and Cell Motility as Early Responses of Cultured Mammalian Cells to Altered Gravitational Vector.International journal of molecular sciences · 2022Article
- Proteomic profiling based classification of CLL provides prognostication for modern therapy and identifies novel therapeutic targets.Blood cancer journal · 2022Article
- Characterization of anticancer drug resistance by reverse-phase protein array: new targets and strategies.Expert review of proteomics · 2022Review
- Reverse phase protein arrays in acute leukemia: investigative and methodological challenges.Expert review of proteomics · 2021Review
- The effects of sample handling on proteomics assessed by reverse phase protein arrays (RPPA): Functional proteomic profiling in leukemia.Journal of proteomics · 2021Article
- Integrative analysis of multi-platform reverse-phase protein array data for the pharmacodynamic assessment of response to targeted therapies.Scientific reports · 2020Article
- RSK inhibitor BI-D1870 inhibits acute myeloid leukemia cell proliferation by targeting mitotic exit.Oncotarget · 2020Article
- Evaluation of antibody responses to the early transcribed membrane protein family in Plasmodium vivax.Parasites & vectors · 2019Article
- A quantitative analysis of heterogeneities and hallmarks in acute myelogenous leukaemia.Nature biomedical engineering · 2019Article
- Mycoplasma contamination of leukemic cell lines alters protein expression determined by reverse phase protein arrays.Cytotechnology · 2018Article
- Recurrent Patterns of Protein Expression Signatures in Pediatric Acute Lymphoblastic Leukemia: Recognition and Therapeutic Guidance.Molecular cancer research : MCR · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
motivationReverse phase protein arrays (RPPA) measure the relative expression levels of a protein in many samples simultaneously. A set of identically spotted arrays can be used to measure the levels of more than one protein. Protein expression within each sample on an array is estimated by borrowing strength across all the samples, but using only within array information. When comparing across slides, it is essential to account for sample loading, the total amount of protein printed per sample. Currently, total protein is estimated using either a housekeeping protein or the sample median across all slides. When the variability in sample loading is large, these methods are suboptimal because they do not account for the fact that the protein expression for each slide is estimated separately.
resultsWe propose a new normalization method for RPPA data, called variable slope (VS) normalization, that takes into account that quantification of RPPA slides is performed separately. This method is better able to remove loading bias and recover true correlation structures between proteins. AVAILABILITY: Code to implement the method in the statistical package R and anonymized data are available at (http://bioinformatics.mdanderson.org/supplements.html).
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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.