TY - JOUR
T1 - Microarray R-based analysis of complex lysate experiments with MIRACLE
AU - List, Markus
AU - Block, Ines
AU - Pedersen, Marlene Lemvig
AU - Christiansen, Helle
AU - Schmidt, Steffen
AU - Thomassen, Mads
AU - Tan, Qihua
AU - Baumbach, Jan
AU - Mollenhauer, J.
N1 - Funding Information:
Funding: This work was supported by the Lundbeckfonden grant for the NanoCAN Center of Excellence in Nanomedicine, the Region Syddanmarks ph.d.-pulje and Forskningspulje, the Fonden Til Lægevidenskabens Fremme and co-financed by the INTERREG 4 A-program Syddanmark-Schleswig-K.E.R.N. with funds from The European Regional Development Fund.
PY - 2014/9/1
Y1 - 2014/9/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84907033279&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btu473
DO - 10.1093/bioinformatics/btu473
M3 - Article
C2 - 25161257
AN - SCOPUS:84907033279
SN - 1367-4803
VL - 30
SP - i631-i638
JO - Bioinformatics
JF - Bioinformatics
IS - 17
ER -