Format

Send to

Choose Destination
Bioinformatics. 2014 Sep 1;30(17):i631-8. doi: 10.1093/bioinformatics/btu473.

Microarray R-based analysis of complex lysate experiments with MIRACLE.

Author information

1
Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, Molecular Oncology, Institute of Molecular Medicine, Human Genetics, Institute of Clinical Research, Epidemiology, Biostatistics and Biodemography, Institute of Public Health and Department of Mathematics and Computer Science, University of Southern Denmark, 5000 Odense, Denmark Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, Molecular Oncology, Institute of Molecular Medicine, Human Genetics, Institute of Clinical Research, Epidemiology, Biostatistics and Biodemography, Institute of Public Health and Department of Mathematics and Computer Science, University of Southern Denmark, 5000 Odense, Denmark Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, Molecular Oncology, Institute of Molecular Medicine, Human Genetics, Institute of Clinical Research, Epidemiology, Biostatistics and Biodemography, Institute of Public Health and Department of Mathematics and Computer Science, University of Southern Denmark, 5000 Odense, Denmark.
2
Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, Molecular Oncology, Institute of Molecular Medicine, Human Genetics, Institute of Clinical Research, Epidemiology, Biostatistics and Biodemography, Institute of Public Health and Department of Mathematics and Computer Science, University of Southern Denmark, 5000 Odense, Denmark Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, Molecular Oncology, Institute of Molecular Medicine, Human Genetics, Institute of Clinical Research, Epidemiology, Biostatistics and Biodemography, Institute of Public Health and Department of Mathematics and Computer Science, University of Southern Denmark, 5000 Odense, Denmark.
3
Lundbeckfonden Center of Excellence in Nanomedicine NanoCAN, Molecular Oncology, Institute of Molecular Medicine, Human Genetics, Institute of Clinical Research, Epidemiology, Biostatistics and Biodemography, Institute of Public Health and Department of Mathematics and Computer Science, University of Southern Denmark, 5000 Odense, Denmark.

Abstract

MOTIVATION:

Reverse-phase protein arrays (RPPAs) allow sensitive quantification of relative protein abundance in thousands of samples in parallel. Typical challenges involved in this technology are antibody selection, sample preparation and optimization of staining conditions. The issue of combining effective sample management and data analysis, however, has been widely neglected.

RESULTS:

This motivated us to develop MIRACLE, a comprehensive and user-friendly web application bridging the gap between spotting and array analysis by conveniently keeping track of sample information. Data processing includes correction of staining bias, estimation of protein concentration from response curves, normalization for total protein amount per sample and statistical evaluation. Established analysis methods have been integrated with MIRACLE, offering experimental scientists an end-to-end solution for sample management and for carrying out data analysis. In addition, experienced users have the possibility to export data to R for more complex analyses. MIRACLE thus has the potential to further spread utilization of RPPAs as an emerging technology for high-throughput protein analysis.

AVAILABILITY:

Project URL: http://www.nanocan.org/miracle/.

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
25161257
PMCID:
PMC4147925
DOI:
10.1093/bioinformatics/btu473
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for Silverchair Information Systems Icon for PubMed Central
Loading ...
Support Center