9,399 research outputs found
A Sustained Dietary Change Increases Epigenetic Variation in Isogenic Mice
Epigenetic changes can be induced by adverse environmental exposures, such as nutritional imbalance, but little is known about the nature or extent of these changes. Here we have explored the epigenomic effects of a sustained nutritional change, excess dietary methyl donors, by assessing genomic CpG methylation patterns in isogenic mice exposed for one or six generations. We find stochastic variation in methylation levels at many loci; exposure to methyl donors increases the magnitude of this variation and the number of variable loci. Several gene ontology categories are significantly overrepresented in genes proximal to these methylation-variable loci, suggesting that certain pathways are susceptible to environmental influence on their epigenetic states. Long-term exposure to the diet (six generations) results in a larger number of loci exhibiting epigenetic variability, suggesting that some of the induced changes are heritable. This finding presents the possibility that epigenetic variation within populations can be induced by environmental change, providing a vehicle for disease predisposition and possibly a substrate for natural selection.This work was supported by the Australian Research Council (DP0771859) and the National Health and Medical Research Council (#459412, #635510)
GenomeGraphs: integrated genomic data visualization with R.
BackgroundBiological studies involve a growing number of distinct high-throughput experiments to characterize samples of interest. There is a lack of methods to visualize these different genomic datasets in a versatile manner. In addition, genomic data analysis requires integrated visualization of experimental data along with constantly changing genomic annotation and statistical analyses.ResultsWe developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. GenomeGraphs uses the biomaRt package to perform on-line annotation queries to Ensembl and translates these to gene/transcript structures in viewports of the grid graphics package. This allows genomic annotation to be plotted together with experimental data. GenomeGraphs can also be used to plot custom annotation tracks in combination with different experimental data types together in one plot using the same genomic coordinate system.ConclusionGenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R
Information visualization for DNA microarray data analysis: A critical review
Graphical representation may provide effective means of making sense of the complexity and sheer volume of data produced by DNA microarray experiments that monitor the expression patterns of thousands of genes simultaneously. The ability to use ldquoabstractrdquo graphical representation to draw attention to areas of interest, and more in-depth visualizations to answer focused questions, would enable biologists to move from a large amount of data to particular records they are interested in, and therefore, gain deeper insights in understanding the microarray experiment results. This paper starts by providing some background knowledge of microarray experiments, and then, explains how graphical representation can be applied in general to this problem domain, followed by exploring the role of visualization in gene expression data analysis. Having set the problem scene, the paper then examines various multivariate data visualization techniques that have been applied to microarray data analysis. These techniques are critically reviewed so that the strengths and weaknesses of each technique can be tabulated. Finally, several key problem areas as well as possible solutions to them are discussed as being a source for future work
Comparison of Clustering Methods for Time Course Genomic Data: Applications to Aging Effects
Time course microarray data provide insight about dynamic biological
processes. While several clustering methods have been proposed for the analysis
of these data structures, comparison and selection of appropriate clustering
methods are seldom discussed. We compared probabilistic based clustering
methods and distance based clustering methods for time course microarray
data. Among probabilistic methods, we considered: smoothing spline clustering
also known as model based functional data analysis (MFDA), functional
clustering models for sparsely sampled data (FCM) and model-based clustering
(MCLUST). Among distance based methods, we considered: weighted gene
co-expression network analysis (WGCNA), clustering with dynamic time warping
distance (DTW) and clustering with autocorrelation based distance (ACF). We
studied these algorithms in both simulated settings and case study data. Our
investigations showed that FCM performed very well when gene curves were short
and sparse. DTW and WGCNA performed well when gene curves were medium or long
( observations). SSC performed very well when there were clusters of gene
curves similar to one another. Overall, ACF performed poorly in these
applications. In terms of computation time, FCM, SSC and DTW were considerably
slower than MCLUST and WGCNA. WGCNA outperformed MCLUST by generating more
accurate and biological meaningful clustering results. WGCNA and MCLUST are the
best methods among the 6 methods compared, when performance and computation
time are both taken into account. WGCNA outperforms MCLUST, but MCLUST provides
model based inference and uncertainty measure of clustering results
EFSIS: Ensemble Feature Selection Integrating Stability
Ensemble learning that can be used to combine the predictions from multiple
learners has been widely applied in pattern recognition, and has been reported
to be more robust and accurate than the individual learners. This ensemble
logic has recently also been more applied in feature selection. There are
basically two strategies for ensemble feature selection, namely data
perturbation and function perturbation. Data perturbation performs feature
selection on data subsets sampled from the original dataset and then selects
the features consistently ranked highly across those data subsets. This has
been found to improve both the stability of the selector and the prediction
accuracy for a classifier. Function perturbation frees the user from having to
decide on the most appropriate selector for any given situation and works by
aggregating multiple selectors. This has been found to maintain or improve
classification performance. Here we propose a framework, EFSIS, combining these
two strategies. Empirical results indicate that EFSIS gives both high
prediction accuracy and stability.Comment: 20 pages, 3 figure
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