Biomedical subjects

Stefanie Scheid

Publications and source records attributed to Stefanie Scheid.

6 recordsLinked to original sources

PubMed2006

OrderedList--a bioconductor package for detecting similarity in ordered gene lists.

UNLABELLED: OrderedList is a Bioconductor compliant package for meta-analysis based on ordered gene lists like those resulting from differential gene expression analysis. Our package quantifies the similarity between gene lists. The significance of the similarity score is estimated from random scores computed on perturbed data. OrderedList illustrates list similarity in intuitive plots and determines the score-driving genes for further analysis. AVAILABILITY: http://www.bioconductor.org CONTACT: claudio.lottaz@molgen.mpg.de SUPPLEMENTARY INFORMATION: Please visit our webpage on http://compdiag.molgen.mpg.de/software.

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PubMed2006

Similarities of ordered gene lists.

MOTIVATION: Many applications of microarray technology in clinical cancer studies aim at detecting molecular features for refined diagnosis. In this paper, we follow an opposite rationale: we try to identify common molecular features shared by phenotypically distinct types of cancer using a meta-analysis of several microarray studies. We present a novel algorithm to uncover that two lists of differentially expressed genes are similar, even if these similarities are not apparent to the eye. The method is based on the ordering in the lists. RESULTS: In a meta-analysis of five clinical microarray studies we were able to detect significant similarities in five of the ten possible comparisons of ordered gene lists. We included studies, where not a single gene can be significantly associated to outcome. The detection of significant similarities of gene lists from different microarray studies is a novel and promising approach. It has the potential to improve upon specialized cancer studies by exploring the power of several studies in one single analysis. Our method is complementary to previous methods in that it does not rely on strong effects of differential gene expression in a single study but on consistent ones across multiple studies.

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PubMed2005

A physiogenomic approach to study the regulation of blood pressure.

Several vasoregulatory systems including the renin-angiotensin system, sympathetic vasoregulation, and cytokine release have been studied extensively. The aim of the present study was to establish a physiogenomic screening model for differentially expressed genes in the regulation of blood pressure that might give a hint as to new vasoregulatory mechanisms. We induced acute hypotension in normotensive rats, assuming that vasoregulatory systems will counteract hypotension. Microarray transcriptome analysis was performed from kidneys 6 h after the induction of acute hypotension. The results were confirmed by real-time PCR. Six functionally known genes (Igfbp1, Xdh, Sult1a1, Mawbp, Por, and Gstm1) and two expressed sequence tages (BI277460 and AI411345) were significantly upregulated. Four of these genes (Igfbp1, Xdh, Por, and Gstm1) have well-characterized functions in the cardiovascular system. The proteins corresponding to Xdh, Por, and Gstm1 are involved in the metabolism of reactive oxygen species (ROS). Because ROS can mediate endothelial dysfunction, we measured the aortic dilatory capacity in thoracic aortic rings. Indeed, vasodilator potency to acetylcholine was largely diminished in hypotensive animals, whereas sodium nitroprusside induced equivalent vasodilations in normotensive and hypotensive animals. The vasodilator potency of the endothelium was partially restored by the superoxide scavenger tiron. Hence, acute hypotension induces a diminished vasodilator potency of the endothelium due to an accelerated degradation of nitric oxide by ROS. The present physiogenomic approach is capable of detecting vasoregulatory mechanisms and may provide deeper insight into the genetics and physiology of blood pressure regulation.

1,2-Dihydroxybenzene-3,5-Disulfonic Acid Disodium ↗

PubMed2005

twilight; a Bioconductor package for estimating the local false discovery rate.

UNLABELLED: twilight is a Bioconductor compatible package for analysing the statistical significance of differentially expressed genes. It is based on the concept of the local false discovery rate (FDR), a generalization of the frequently used global FDR. twilight implements the heuristic search algorithm for estimating the local FDR introduced in our earlier work. In addition to the raw significance measures, it produces diagnostic plots, which provide insight into the extent of differential expression across genes. AVAILABILITY: http://www.bioconductor.org CONTACT: stefanie.scheid@molgen.mpg.de SUPPLEMENTARY INFORMATION: Please visit our software webpage on http://compdiag.molgen.mpg.de/software.

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PubMed2003

Expression profiling of human idiopathic dilated cardiomyopathy.

OBJECTIVE: To investigate the global changes accompanying human dilated cardiomyopathy (DCM) we performed a large-scale expression screen using myocardial biopsies from a group of DCM patients with moderate heart failure. By hierarchical clustering and functional annotation of the deregulated genes we examined extensive changes in the cellular and molecular processes associated to DCM. METHODS: The expression profiles were obtained using a whole genome covering library (UniGene RZPD1) comprising 30336 cDNA clones and amplified RNA from myocardiac biopsies from 10 DCM patients in comparison to tissue samples from four non-failing, healthy donors. RESULTS: By setting stringent selection criteria 364 differentially expressed, sequence-verified non-redundant transcripts were identified with a false discovery rate of <0.001. Numerous genes and ESTs were identified representing previously recognised, as well as novel DCM-associated transcripts. Many of them were found to be upregulated and involved in cardiomyocyte energetics, muscle contraction or signalling. Two hundred and twenty-two deregulated transcripts were functionally annotated and hierarchically clustered providing an insight into the pathophysiology of DCM. Data was validated using the MLP-deficient mouse, in which several differentially expressed transcripts identified in the human DCM biopsies could be confirmed. CONCLUSIONS: We report the first genome-wide expression profile analysis using cardiac biopsies from DCM patients at various stages of the disease. Although there is a diversity of links between the cytoskeleton and the initiation of DCM, we speculate that genes implicated in intracellular signalling and in muscle contraction are associated with early stages of the disease. Altogether this study represents the most comprehensive and inclusive molecular portrait of human cardiomyopathy to date.

Adult↗

PubMedDate not supplied

A stochastic downhill search algorithm for estimating the local false discovery rate.

Screening for differential gene expression in microarray studies leads to difficult large-scale multiple testing problems. The local false discovery rate is a statistical concept for quantifying uncertainty in multiple testing. In this paper, we introduce a novel estimator for the local false discovery rate that is based on an algorithm which splits all genes into two groups, representing induced and noninduced genes, respectively. Starting from the full set of genes, we successively exclude genes until the gene-wise p-values of the remaining genes look like a typical sample from a uniform distribution. In comparison to other methods, our algorithm performs compatibly in detecting the shape of the local false discovery rate and has a smaller bias with respect to estimating the overall percentage of noninduced genes. Our algorithm is implemented in the Bioconductor compatible R package TWILIGHT version 1.0.1, which is available from http://compdiag.molgen.mpg.de/software or from the Bioconductor project at http://www.bioconductor.org.

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