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Number of citations per year for the bioinformatics software tool ArrayNorm
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Protocols

ArrayNorm specifications

Information


Unique identifier OMICS_26964
Name ArrayNorm
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 1.7.6
Stability Beta
Maintained Yes

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Documentation


Maintainers


  • person_outline Zlatko Trajanoski
  • person_outline Gerhard Thallinger

Publication for ArrayNorm

ArrayNorm citations

 (13)
library_books

Comprehensive Analysis of miRNome Alterations in Response to Sorafenib Treatment in Colorectal Cancer Cells

2016
Int J Mol Sci
PMCID: 5187811
PMID: 27916938
DOI: 10.3390/ijms17122011

[…] 00B microarray scanner (Molecular Devices, Sunnyvale, CA, USA) at 10 µm resolution and the resultant TIFF images were analyzed with GenePix Pro 4.1 software. Raw data was subsequently processed using ArrayNorm for normalization [] and Genesis software for evaluation []. Up- or down-regulation of individual miRNAs was tested by employing a one-sample t-test using the log2-transformed expression rat […]

library_books

Let 7i 5p represses brite adipocyte function in mice and humans

2016
Sci Rep
PMCID: 4921928
PMID: 27345691
DOI: 10.1038/srep28613

[…] d by pre-processing to filter out low intensity, saturated and in homogenous spots. Background correction and normalization (global mean followed by dye-swap pair normalization) were performed, using ArrayNorm software. The resulting log2-fold changes of miRNAs (calculated against the common reference sample) were further analysed and visualized using R (www.r-project.org). Normalized as well as r […]

library_books

miR 125b affects mitochondrial biogenesis and impairs brite adipocyte formation and function

2016
PMCID: 5021678
PMID: 27656399
DOI: 10.1016/j.molmet.2016.06.005

[…] nd day 16. Detailed protocols for sample labeling and hybridization were performed as described in . Further, the raw data was background corrected, normalized by global mean and dye–swap pairs using ArrayNorm , and then exported as text-file containing log2 transformed ratios of gene expression. Filtering for present values and differential expression was conducted with Genesis software . All exp […]

library_books

SaDA: From Sampling to Data Analysis—An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High Throughput Microarray Data

2015
PMCID: 4483705
PMID: 26047146
DOI: 10.3390/ijerph120606352

[…] ] are meaningful in big laboratories which, besides data analysis, are involved in protocol development, data acquisition and data sharing. Freely available tools for microarray analysis like TM4 [], ArrayNorm [], ArrayPipe [] GPR-Analyzer [] have either become obsolete or lack key features in terms of extensibility and integration with analysis tools, like R and modern graphing libraries. In the […]

library_books

Effects of Oxidized Phospholipids on Gene Expression in RAW 264.7 Macrophages: A Microarray Study

2014
PLoS One
PMCID: 4204898
PMID: 25333283
DOI: 10.1371/journal.pone.0110486

[…] p, corresponding to three independent experiments (biological replicates). Features were filtered for low-quality spots and arrays were global mean and dye-swap normalized, and log2-transformed using ArrayNorm . Genes with >1.5 fold change and adjusted p-value (FDR) <0.05 were considered significantly differentially expressed using the R/Bioconductor package limma. Microarray data are available in […]

library_books

MiR 200a regulates epithelial to mesenchymal transition related gene expression and determines prognosis in colorectal cancer patients

2014
Br J Cancer
PMCID: 3960623
PMID: 24504363
DOI: 10.1038/bjc.2014.51

[…] 0B microarray scanner (Molecular Devices, Sunnyvale, CA, USA) at 10 μm resolution and the resultant TIFF images were analysed with GenePix Pro 4.1 software. Raw data were subsequently processed using ArrayNorm () for normalisation and Genesis software for evaluation (). All experimental parameters, raw and processed data files were submitted to the public repository Gene Expression Omnibus (GEO ac […]


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ArrayNorm institution(s)
Institute of Genomics and Bioinformatics and Christian Doppler Laboratory for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria; Department of Biomolecular Sciences, UMIST, Manchester, UK
ArrayNorm funding source(s)
Supported by the Austrian GEN-AU project BIN (Bioinformatics Integration Network) and by the EU Marie Curie Training Site grant Genomics of Lipid Metabolism.

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