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Visualisation of Gene Expression Data Ã¢ÂÂ the GE-biplot, the Chip-plot and the Gene-plot

Pittelkow, Yvonne; Wilson, Susan - In: Statistical Applications in Genetics and Molecular Biology 2 (2007) 1, pp. 6-6

Visualisation methods for exploring microarray data are particularly important for gaining insight into data from gene …. Further, good visualisation techniques are useful for outlier detection in microarray data and for aiding biological … display of microarray data as both the genes and the chips can be simultaneously plotted. In this paper we describe several …

Persistent link: https://www.econbiz.de/10005046577

Early Diagnostic Marker Panel Determination for Microarray Based Clinical Studies

Jaeger, Jochen; Weichenhan, Dieter; Ivandic, Boris; … - In: Statistical Applications in Genetics and Molecular Biology 4 (2007) 1, pp. 9-9

We present a novel, cost efficient two-phase design for predictive clinical gene expression studies: early marker panel determination (EMPD). In Phase-1, genome-wide microarrays are used only for a small number of individual patient samples. From this Phase-1 data a panel of marker genes is...

Persistent link: https://www.econbiz.de/10005046621

Orthology-Based Multilevel Modeling of Differentially Expressed Mouse and Human Gene Pairs

Ogorek, Benjamin; Stefanski, Leonard - In: Statistical Applications in Genetics and Molecular Biology 8 (2009) 1, pp. 2-2

There is great interest in finding human genes expressed through pharmaceutical intervention, thus opening a genomic window into benefit and side-effect profiles of a drug. Human insight gained from FDA-required animal experiments has historically been limited, but in the case of gene expression...

Persistent link: https://www.econbiz.de/10005585054

Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data

JÃÂ¶rg RahnenfÃÂ¼hrer; Domingues, Francisco; … - In: Statistical Applications in Genetics and Molecular Biology 3 (2007) 1, pp. 16-16

findings from microarray experiments.Recently introduced methods test if members of predefined gene sets are enriched in a list … of top-ranked genes in a microarray study. We improve this approach by defining scores that depend on all members of the …

Persistent link: https://www.econbiz.de/10005585090

Statistical Significance Threshold Criteria For Analysis of Microarray Gene Expression Data

Cheng, Cheng; Pounds, Stanley; Boyett, James; Pei, Deqing; … - In: Statistical Applications in Genetics and Molecular Biology 3 (2007) 1, pp. 36-36

The methodological advancement in microarray data analysis on the basis of false discovery rate (FDR) control, such as …

Persistent link: https://www.econbiz.de/10005752555

Incorporating Duplicate Genotype Data into Linear Trend Tests of Genetic Association: Methods and Cost-Effectiveness

Borchers, Bryce; Brown, Marshall; McLellan, Brian; … - In: Statistical Applications in Genetics and Molecular Biology 8 (2009) 1, pp. 24-24

instead of spending the same money to increase the sample size. Duplicate genotyping is particularly cost-effective when SNP …

Persistent link: https://www.econbiz.de/10005046603

Detecting Local High-Scoring Segments: a First-Stage Approach for Genome-Wide Association Studies

Guedj, Mickael; Robelin, David; Hoebeke, Mark; … - In: Statistical Applications in Genetics and Molecular Biology 5 (2007) 1, pp. 22-22

Genetic epidemiology aims at identifying biological mechanisms responsible for human diseases. Genome-wide association studies, made possible by recent improvements in genotyping technologies, are now promisingly investigated. In these studies, common first-stage strategies focus on marginal...

Persistent link: https://www.econbiz.de/10005046611

A Probabilistic Approach to Large-Scale Association Scans: A Semi-Bayesian Method to Detect Disease-Predisposing Alleles

Schrodi, Steven - In: Statistical Applications in Genetics and Molecular Biology 4 (2007) 1, pp. 31-31

Recent analytic and technological breakthroughs have set the stage for genome-wide linkage disequilibrium studies to map disease-susceptibility variants. This paper discusses a probabilistic methodology for making disease-mapping inferences in large-scale case-control genetic studies. The...

Persistent link: https://www.econbiz.de/10005246477

Empirical Bayes Microarray ANOVA and Grouping Cell Lines by Equal Expression Levels

Ingrid LÃÂ¶nnstedt; Rimini, Rebecca; Nilsson, Peter - In: Statistical Applications in Genetics and Molecular Biology 4 (2007) 1, pp. 7-7

research. The usual F-statistic is unsatisfactory for microarray data, which explore many thousand genes in parallel, with few …

Persistent link: https://www.econbiz.de/10005046615

Saturation and Quantization Reduction in Microarray Experiments using Two Scans at Different Sensitivities

Jorge GarcÃÂa de la Nava; Hijum, Sacha van; … - In: Statistical Applications in Genetics and Molecular Biology 3 (2007) 1, pp. 11-11

We present a mathematical model to extend the dynamic range of gene expression data measured by laser scanners. The strategy is based on the rather simple but novel idea of producing two images with different scanner sensitivities, obtaining two different sets of expression values: the first is...

Persistent link: https://www.econbiz.de/10005585060