Evidence map›Paper›PMID 25161257›Full record

ArticleBioinformatics (Oxford, England)2014

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

Markus List, Ines Block, Marlene Lemvig Pedersen, Helle Christiansen, Steffen Schmidt, Mads Thomassen, Qihua Tan, Jan Baumbach, Jan Mollenhauer

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Markus ListLundbeckfonden 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.
Ines BlockLundbeckfonden 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.
Marlene Lemvig PedersenLundbeckfonden 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.
Helle ChristiansenLundbeckfonden 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.
Steffen SchmidtLundbeckfonden 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.
Mads ThomassenLundbeckfonden 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.
Qihua TanLundbeckfonden 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.
Jan BaumbachLundbeckfonden 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.
Jan MollenhauerLundbeckfonden 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.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

motivationReverse-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.

resultsThis 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.

Indexed as

SoftwareCell ExtractsInternetProtein Array AnalysisProteinsCell ExtractsProteins

Identifiers

PMID25161257
PMCPMC4147925

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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.