Analysis of multiplex gene expression maps obtained by voxelation

BackgroundGene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions.ResultsTo analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in cortex and corpus callosum.ConclusionThe experimental results confirm the hypothesis that genes with similar gene expression maps might have similar gene functions. The voxelation data takes into account the location information of gene expression level in mouse brain, which is novel in related research. The proposed approach can potentially be used to predict gene functions and provide helpful suggestions to biologists

Learning pair-wise gene functional similarity by multiplex gene expression maps

Abstract Background The relationships between the gene functional similarity and gene expression profile, and between gene function annotation and gene sequence have been studied extensively. However, not much work has considered the connection between gene functions and location of a gene's expression in the mammalian tissues. On the other hand, although unsupervised learning methods have been commonly used in functional genomics, supervised learning cannot be directly applied to a set of normal genes without having a target (class) attribute. Results Here, we propose a supervised learning methodology to predict pair-wise gene functional similarity from multiplex gene expression maps that provide information about the location of gene expression. The features are extracted from expression maps and the labels denote the functional similarities of pairs of genes. We make use of wavelet features, original expression values, difference and average values of neighboring voxels and other features to perform boosting analysis. The experimental results show that with increasing similarities of gene expression maps, the functional similarities are increased too. The model predicts the functional similarities between genes to a certain degree. The weights of the features in the model indicate the features that are more significant for this prediction. Conclusions By considering pairs of genes, we propose a supervised learning methodology to predict pair-wise gene functional similarity from multiplex gene expression maps. We also explore the relationship between similarities of gene maps and gene functions. By using AdaBoost coupled with our proposed weak classifier we analyze a large-scale gene expression dataset and predict gene functional similarities. We also detect the most significant single voxels and pairs of neighboring voxels and visualize them in the expression map image of a mouse brain. This work is very important for predicting functions of unknown genes. It also has broader applicability since the methodology can be applied to analyze any large-scale dataset without a target attribute and is not restricted to gene expressions

Statistical Analysis of Multiplex Brain Gene Expression Images

Analysis of variance (ANOVA) was employed to investigate 9,000 gene expression patterns from brains of both normal mice and mice with a pharmacological model of Parkinson's disease (PD). The data set was obtained using voxelation, a method that allows high-throughput acquisition of 3D gene expression patterns through analysis of spatially registered voxels (cubes). This method produces multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems. The ANOVA model was compared to the results from singular value decomposition (SVD) by using the first 42 singular vectors of the data matrix, a number equal to the rank of the ANOVA model. The ANOVA was also compared to the results from non-parametric statistics. Lastly, images were obtained for a subset of genes that emerged from the ANOVA as significant. The results suggest that ANOVA will be a valuable framework for insights into the large number of gene expression patterns obtained from voxelation.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45422/1/11064_2004_Article_454311.pd

Developing an Integrative Glycobiology Workflow for the Identification of Disease Markers for Pancreatic Cancer

A deeper understanding of dysregulated glycosylation in pancreatic cancer can provide insights into disease mechanisms and the identification of novel disease markers. Recent improvements in mass spectrometry techniques have been instrumental in profiling biologically relevant tissue sections in order to identify disease marker candidates, but have either not yet been adopted for studying glycosylation or applied directly to pancreatic cancer. In the dissertation herein, new methods have been developed and adapted to the study of aberrant glycosylation in pancreatic cancer, with the ultimate goal of identifying novel disease marker candidates. For the first time, we describe a mass spectrometry imaging approach to study the localization of N-glycans. This technique demonstrated a histology-derived localization of N-glycans across tissue sections, with identifications displaying remarkable consistency with documented studies. Furthermore, the technique provides superior structural information compared to preexisting methodologies. In the analysis of diseased specimen, changes in glycosylation can be linked to aberrations in glycosyltransferase expression. When applied to pancreatic cancer in a high-throughput and high-dimensional analysis, panels of glycans displayed an improved ability to differentiate tumor from non-tumor tissues compared to current disease markers. Furthermore, the data suggest that glycosylation can identify premalignant lesions, as well as differentiate between malignant and benign conditions. These observations overcome significant limitations that hinder the efficacy of current disease markers. In an effort to link aberrant glycosylation to the modified protein, a subset of glycosylated proteins were enriched and analyzed by mass spectrometry to identify proteins that are integral to disease progression and can be probed for the early detection of pancreatic cancer. Known disease markers were among the glycoproteins identified, validating the utility of the enrichment and detection strategy outlined. This approach also differentiated the role of N- and O-glycosylation in antigen expression. Finally, we outline an integrated workflow that takes advantage of the unique capabilities of high resolution mass spectrometers. This workflow can capitalize on prior glycomic and proteomic experiments to provide a comprehensive analysis of dysregulated protein glycosylation in pancreatic cancer

Analysis of multiplex gene expression maps obtained by voxelation.

BackgroundGene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acquisition of genome-wide atlases of expression patterns in the mouse brain. On the other hand, some work has been performed on studying gene functions, without taking into account the location information of a gene's expression in a mouse brain. In this paper, we present an approach for identifying the relation between gene expression maps obtained by voxelation and gene functions.ResultsTo analyze the dataset, we chose typical genes as queries and aimed at discovering similar gene groups. Gene similarity was determined by using the wavelet features extracted from the left and right hemispheres averaged gene expression maps, and by the Euclidean distance between each pair of feature vectors. We also performed a multiple clustering approach on the gene expression maps, combined with hierarchical clustering. Among each group of similar genes and clusters, the gene function similarity was measured by calculating the average gene function distances in the gene ontology structure. By applying our methodology to find similar genes to certain target genes we were able to improve our understanding of gene expression patterns and gene functions. By applying the clustering analysis method, we obtained significant clusters, which have both very similar gene expression maps and very similar gene functions respectively to their corresponding gene ontologies. The cellular component ontology resulted in prominent clusters expressed in cortex and corpus callosum. The molecular function ontology gave prominent clusters in cortex, corpus callosum and hypothalamus. The biological process ontology resulted in clusters in cortex, hypothalamus and choroid plexus. Clusters from all three ontologies combined were most prominently expressed in cortex and corpus callosum.ConclusionThe experimental results confirm the hypothesis that genes with similar gene expression maps might have similar gene functions. The voxelation data takes into account the location information of gene expression level in mouse brain, which is novel in related research. The proposed approach can potentially be used to predict gene functions and provide helpful suggestions to biologists

Technology 2001: The Second National Technology Transfer Conference and Exposition, volume 2

Proceedings of the workshop are presented. The mission of the conference was to transfer advanced technologies developed by the Federal government, its contractors, and other high-tech organizations to U.S. industries for their use in developing new or improved products and processes. Volume two presents papers on the following topics: materials science, robotics, test and measurement, advanced manufacturing, artificial intelligence, biotechnology, electronics, and software engineering