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BACKGROUND The requirement of a large amount of high-quality RNA is a major limiting factor for microarray experiments using biopsies. An average microarray experiment requires 10-100 microg of RNA. However, due to their small size, most biopsies do not yield this amount. Several different approaches for RNA amplification in vitro have been described and(More)
BACKGROUND The increasing number of gene expression microarray studies represents an important resource in biomedical research. As a result, gene expression based diagnosis has entered clinical practice for patient stratification in breast cancer. However, the integration and combined analysis of microarray studies remains still a challenge. We assessed the(More)
arrayMagic is a software package for quality control and preprocessing of two-colour cDNA microarray data. The automated analysis pipeline comprises data import, normalization, replica merging, quality diagnostics and data export. The script-based processing combines reproducibility and flexibility at high-throughput and provides quality-assured and(More)
The matter of concern are algorithms for the discrimination of direct from indirect regulatory effects from an interaction graph built up by error-prone measurements. Many of these algorithms can be cast as a rule for the removal of a single edge of the graph, such that the remaining graph is still consistent with the data. A set of mild conditions is given(More)
MOTIVATION In cancer, chromosomal imbalances like amplifications and deletions, or changes in epigenetic mechanisms like DNA methylation influence the transcriptional activity. These alterations are often not limited to a single gene but affect several genes of the genomic region and may be relevant for the disease status. For example, the ERBB2 amplicon(More)
UNLABELLED arrayMagic is a software package for quality control and preprocessing of two-colour cDNA microarray data. The automated analysis pipeline comprises data import, normalization, replica merging, quality diagnostics and data export. The script-based processing combines reproducibility and flexibility at high-throughput and provides quality-assured(More)
BACKGROUND Aquaporins (AQPs) have been recognized to promote tumor progression, invasion, and metastasis and are therefore recognized as promising targets for novel anti-cancer therapies. Potentially relevant AQPs in distinct cancer entities can be determined by a comprehensive expression analysis of the 13 human AQPs. METHODS We analyzed the presence of(More)
Neuropathic pain, caused by a lesion in the somatosensory system, is a severely impairing mostly chronic disease. While its underlying molecular mechanisms are not thoroughly understood, neuroimmune interactions as well as changes in the pain pathway such as sensitization of nociceptors have been implicated. It has been shown that not only are different(More)
Clinically, the differentiation between ischemic (ICM) and nonischemic (NICM) human cardiomyopathies is highly relevant, because ICM and NICM differ with respect to prognosis and certain aspects of pharmacological therapy, despite a common final phenotype characterized by ventricular dilatation and reduced contractility. So far, it is unclear whether(More)
Early and accurate pre-clinical and clinical biomarkers of hepatotoxicity facilitate the drug development process and the safety monitoring in clinical studies. We selected eight known model compounds to be administered to male Wistar rats to identify biomarkers of drug induced liver injury (DILI) using transcriptomics, metabolite profiling (metabolomics)(More)
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