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PAA specifications


Unique identifier OMICS_11088
Name PAA
Alternative name Protein Array Analyzer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data PAA imports microarray data in gpr file format.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 1.14.0
Stability Stable
limma, gplots, BiocGenerics, BiocStyle, RUnit, gtools, MASS, vsn, ROCR, e1071, sva, randomforest, R(>=3.2.0), Rcpp(>=0.11.6), mRMRe
Maintained Yes


No version available



  • person_outline Michael Turewicz

Publication for Protein Array Analyzer

PAA citations


Neurofibromin knockdown in glioma cell lines is associated with changes in cytokine and chemokine secretion in vitro

Sci Rep
PMCID: 5895785
PMID: 29643433
DOI: 10.1038/s41598-018-24046-2

[…] g from 15 seconds to 10 minutes. Film was scanned using an Epson Perfection V78 Pro transmission mode scanner and Epson SilverFast software. Signal levels were measured using ImageJ software with the Protein Array Analyzer plugin. Values from duplicate spots were averaged, and the relative signal was calculated in siNF1 treated sample, compared to siControl treated cells. […]


Response of human normal and leukemia cells to factors released by amnion fragments in vitro

PLoS One
PMCID: 5875856
PMID: 29596519
DOI: 10.1371/journal.pone.0195035

[…] e array was visualized with a chemiluminescence imaging system (UVP camera GelDocDC Imaging System, BioRad, CA USA), and densitometry analysis was performed with free software: ImageJ with plugin the Protein Array Analyzer (NIH, Bethesda, MD, USA). Fluorescence values (FV) were measured and calculated as follows:FV = fluorescence of growth factor–MNC/MPC, where MNC–mean of negative control (4 samp […]


An optimized method using peptide arrays for the identification of in vitro substrates of lysine methyltransferase enzymes

PMCID: 5814365
PMID: 29487803
DOI: 10.1016/j.mex.2018.01.012

[…] 1. Open the ImageJ program and install the ‘Protein Array Analyzer’ macro by clicking on the “toolsets” menu icon of the ImageJ tool bar. If this is not available, download the macro directly ( and fol […]


Liraglutide restores chronic ER stress, autophagy impairments and apoptotic signalling in SH SY5Y cells

Sci Rep
PMCID: 5700973
PMID: 29170452
DOI: 10.1038/s41598-017-16488-x

[…] th LumiGLO®/Peroxide Reagent were used to visualise the bound antibody cocktail by chemiluminescence. ChemiDoc™ MP Imaging System with Image Lab™ software was used to capture images of the slide. The Protein Array Analyzer for Image J (National Institutes of Health, Bethesda, Maryland, USA) was used for the densitometric analysis. The relative peak intensities of the examined signalling molecules […]


Melanoma topology reveals a stem like phenotype that promotes angiogenesis

Sci Adv
PMCID: 5656422
PMID: 29075670
DOI: 10.1126/sciadv.1701350

[…] cked membranes overnight with the membranes at 4°C. Prepared membranes were exposed to an x-ray film and developed for the protein detection. Films were scanned and analyzed using the ImageJ plug-in “Protein array analyzer” (written by G. Carpentier, 2010; […]


Activated macrophages control human adipocyte mitochondrial bioenergetics via secreted factors

PMCID: 5641636
PMID: 29031722
DOI: 10.1016/j.molmet.2017.07.008

[…] ted for Odyssey System (LiCor) according to manufacturer's recommendation. Quantification, background correction and normalization of fluorescent signals were performed with ImageJ software using the Protein Array Analyzer tool set . […]


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PAA institution(s)
Proteom-Center, Ruhr-University Bochum, Bochum, Germany
PAA funding source(s)
This work was supported by P.U.R.E., a project of Nordrhein-Westfalen, a federal state of Germany; and de.NBI, a project of the German Federal Ministry of Education and Research (BMBF) [grant number FKZ 031 A 534A].

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