ArticleBioinformatics (Oxford, England)2015
Development of a robust classifier for quality control of reverse-phase protein arrays.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 53 citations in OpenAlex.
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- Actinomycin D and bortezomib disrupt protein homeostasis in Wilms tumor.bioRxiv : the preprint server for biology · 2024Article
- A protein expression atlas on tissue samples and cell lines from cancer patients provides insights into tumor heterogeneity and dependencies.Nature cancer · 2024Article
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- Global proteomic identifies multiple cancer-related signaling pathways altered by a gut pathobiont associated with colorectal cancer.Scientific reports · 2023Article
- RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data.Bioinformatics (Oxford, England) · 2022Article
- Tumor-intrinsic SIRPA promotes sensitivity to checkpoint inhibition immunotherapy in melanoma.Cancer cell · 2022Article
- The molecular heterogeneity of the precancerous breast affects drug efficacy.Scientific reports · 2022Article
- Multi-modal molecular programs regulate melanoma cell state.Nature communications · 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
- 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
- Summit: Automated Analysis of Arrayed Single-Cell Gel Electrophoresis.SLAS technology · 2021Article
Corrections and comments
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Authors and funding
11 authors at 1 institution in 1 country.
Funding
Abstract
motivationHigh-throughput reverse-phase protein array (RPPA) technology allows for the parallel measurement of protein expression levels in approximately 1000 samples. However, the many steps required in the complex protocol (sample lysate preparation, slide printing, hybridization, washing and amplified detection) may create substantial variability in data quality. We are not aware of any other quality control algorithm that is tuned to the special characteristics of RPPAs.
resultsWe have developed a novel 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. After training, we tested the classifier using two independent validation datasets. We conclude that the classifier can distinguish RPPA slides of good quality from those of poor quality sufficiently well such that normalization schemes, protein expression patterns and advanced biological analyses will not be drastically impacted by erroneous measurements or systematic variations. AVAILABILITY AND IMPLEMENTATION: The classifier, implemented in the "SuperCurve" R package, can be freely downloaded at http://bioinformatics.mdanderson.org/main/OOMPA:Overview or http://r-forge.r-project.org/projects/supercurve/. The data used to develop and validate the classifier are available at http://bioinformatics.mdanderson.org/MOAR.
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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.