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Use of SNP-Arrays for ChIP Assays: Computational Aspects

Use of SNP-Arrays for ChIP Assays: Computational Aspects

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作者： Enrique M. Muro Jennifer A. McCann Michael A. Rudnicki Miguel A. Andrade-Navarro

The simultaneous genotyping of thousands of single nucleotide polymorphisms (SNPs) in a genome using SNP-Arrays is a very important tool that is revolutionizing genetics and molecular biology. We expanded the utility of this technique by using it following chromatin immunoprecipitation (ChIP) to assess the multiple genomic locations protected by a protein complex recognized by an antibody. The power of this technique is illustrated through an analysis of the changes in histone H4 acetylation, a marker of open chromatin and transcriptionally active genomic regions, which occur during differentiation of human myoblasts into myotubes. The findings have been validated by the observation of a significant correlation between the detected histone modifications and the expression of the nearby genes, as measured by DNA expression microarrays. This chapter focuses on the computational analysis of the data. less

关键词： Microarray ChIP Assay Nucleic Acid Microarray Genotyping SNP Microarray Statistical Calculation Genome Analysis Data analysis Ensembl programming language Homo sapiens histone Chromatin acetylation single nucleotide polymorphism database analysis

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Comparing 2D Electrophoretic Gels Across Internet Databases: An Open Source Application

Comparing 2D Electrophoretic Gels Across Internet Databases:...

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作者： Peter F. Lemkin Gregory C. Thornwall Jai A. Evans

In (1–4) and in the second edition of this book (5), we described a Web-based computer-assisted visual method called Flicker for comparing two two-dimensional (2D) protein gel images across the Internet using a Java ... 详细信息

关键词： Image Processing Recombinant Protein Expression Gel Electrophoresis Mass Spectrometry Fractionation Image Analysis Image Enhancement Microarray Expasy Pull-down Assay programming language

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Integration of Diverse Microarray Data Types

Integration of Diverse Microarray Data Types

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作者： Keyan Salari Jonathan R. Pollack

Over the past decade, DNA microarrays have proven to be a powerful tool in biological research for the molecular surveillance of cells and tissues. The expansive utility of DNA microarrays owes its nascence to the development of a multitude of microarray platforms that enable the systematic and comprehensive exploration of diverse genomic properties and processes. Concomitant with the explosive generation of microarray data over the last several years has been an increasing interest in the integration of such diverse data types, thus spurring the development of novel statistical techniques and integrative bioinformatics tools. This chapter will outline general approaches to microarray data integration and provide an introduction to DR-Integrator, a broadly useful analysis tool for the integration of DNA copy number and gene-expression microarray data. less

关键词： Microarray Comparative Genomic Hybridization Genomics Microarray Statistical Calculation programming language Data integration gene-expression DR-Integrator

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Microarrayed Allergen Molecules for Diagnostics of Allergy

Microarrayed Allergen Molecules for Diagnostics of Allergy

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作者： Jing Lin Ludmilla Bardina Wayne G. Shreffler

With the evolution of peptide synthesis techniques and microarray technology, it is now possible to map and characterize allergenic epitopes on a microarray platform. The peptide microarray-based immunoassay allows simultaneous analysis of thousands of target peptides using small volumes of diluted serum samples, and has a promising future to become a superior testing tool for aspects of food allergy diagnosis and prognosis, as well as for designing recombinant allergens for safe immunotherapy. Characterization of allergenic epitopes provides fundamental knowledge for understanding mechanisms of food allergy. This chapter describes in detail the development of a sensitive and reliable peptide microarray-based immunoassay. The information includes a comparison of different slide substrates, effect of buffers on spot morphology, performance of printing pins, immunolabeling detection systems with different levels of sensitivity, and suggested approaches to data analysis. less

关键词： Microarray Peptide Array Epitope Mapping Immunolabeling Peptide Synthesis Microarray Immunoassay Dialysis Data analysis programming language Allergy diagnosis Anti-human IgE Anti-biotin Anti-FITC Anti-human

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Phylogenomic Analysis of EST Datasets

Phylogenomic Analysis of EST Datasets

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作者： José M. Peregrín-Alvarez John Parkinson

To date the genomes of over 600 organisms have been generated of which 100 are from eukaryotes. Together with partial genome data for an additional 700 eukaryotic organisms, these exceptional sequence resources offer new opportunities to explore phylogenetic relationships and species diversity. The identification of highly diverse sequences specific to an EST-based sequence dataset offers insights into the extent of genetic novelty within that dataset. Sequences that are only shared with other related species from the same taxon might represent genes associated with taxon-specific innovations. On the other hand, sequences that are highly conserved across many other species offer valuable resources for performing more in-depth phylogenetic analyses. In the following chapter, we guide the reader through the process of examining their sequence datasets in the context of phylogenetic relationships. Performed across large-scale datasets, such analyses are termed Phylogenomics. Two complementary approaches are described, both based on the use of BLAST similarity metrics. The first uses an established Java tool – SimiTri – to visualize sequence similarity relationships between the EST dataset and three user-defined datasets. The second focuses on the use of phylogenetic profiles to identify groups of taxonomically related sequences. less

关键词： Genomics Sequence Similarity Search Sequence Comparison programming language Echinococcus multilocularis bioinformatics clustering Expressed sequence tags ESTs phylogenetic profiles

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Co-expression Analysis of Metabolic Pathways in Plants

Co-expression Analysis of Metabolic Pathways in Plants

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作者： Ann Loraine

Co-expression analysis allows experimenters to re-use archived expression microarray data to uncover previously unknown functional relationships between genes. An observation that a group of genes are co-expressed across diverse experimental conditions suggests they may play similar roles in the cell. Several thousand expression microarray experiments performed on samples from Arabidopsis thaliana have entered the public domain and it is now possible to use these data to investigate metabolic networks in plants. This chapter explains how to use a Web-based tool (CressExpress) to investigate co-expression of genes involved in metabolic pathways in Arabidopsis. Using CressExpress together with desktop visualization and analysis tools, one can easily identify clusters of genes that are co-expressed with one or more genes of interest, making it possible to identify new players in metabolic pathways that are regulated at the level of mRNA abundance. less

关键词： Microarray Statistical Calculation programming language co-expression Expression array correlation linear regression relevance networks

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Computational reconstruction of cell and tissue surfaces for modeling and data analysis

Computational reconstruction of cell and tissue surfaces for...

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作者： Frederick Klauschen Hai Qi Jackson G Egen Ronald N Germain Martin Meier-Schellersheim

We present a method for the computational reconstruction of the 3-D morphology of biological objects, such as cells, cell conjugates or 3-D arrangements of tissue structures, using data from high-resolution microscopy modalities. The method is based on the iterative optimization of Voronoi representations of the spatial structures. The reconstructions of biological surfaces automatically adapt to morphological features of varying complexity with flexible degrees of resolution. We show how 3-D confocal images of single cells can be used to generate numerical representations of cellular membranes that may serve as the basis for realistic, spatially resolved computational models of membrane processes or intracellular signaling. Another example shows how the protocol can be used to reconstruct tissue boundaries from segmented two-photon image data that facilitate the quantitative analysis of lymphocyte migration behavior in relation to microanatomical structures. Processing time is of the order of minutes depending on data features and reconstruction parameters. less

关键词： Microscopy Surface Rendering Fluorescence Microscopy Confocal Microscopy Data analysis programming language Malus domestica

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Identification of

Identification of

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作者： Leonardo Mariño-Ramírez Kannan Tharakaraman Olivier Bodenreider John Spouge David Landsman

Reliable identification and assignment of cis-regulatory elements in promoter regions is a challenging problem in biology. The sophistication of transcriptional regulation in higher eukaryotes, particularly in metazoans, could be an important factor contributing to their organismal complexity. Here we present an integrated approach where networks of co-expressed genes are combined with gene ontology–derived functional networks to discover clusters of genes that share both similar expression patterns and functions. Regulatory elements are identified in the promoter regions of these gene clusters using a Gibbs sampling algorithm implemented in the A-GLAM software package. Using this approach, we analyze the cell-cycle co-expression network of the yeast Saccharomyces cerevisiae, showing that this approach correctly identifies cis-regulatory elements present in clusters of co-expressed genes. less

关键词： Microarray Simulated Annealing Cytoscape Multiple Sequence Alignment programming language gene ontology networks Promoter sequences co-expression transcription factor–binding sites Gibbs sampling

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In Vivo Measurements of Cytosolic Calcium in

In Vivo Measurements of Cytosolic Calcium in

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作者： Claire Y. Allan Paul R. Fisher

The involvement of calcium signalling during chemotaxis in Dictyostelium discoideum is well documented. Spatiotemporal increases of intracellular calcium ([Ca2+]i) have been observed within seconds of stimulation with the chemoattractants folic acid and cAMP. This rise in [Ca2+]i localises to the rear cortex of the cell (J. Cell Sci. 109:2673–2678, 1996) and has been found to be not essential for chemotaxis, but likely to be involved in fine tuning of chemotactic responses (EMBO J. 19:4846–4854, 2000). Measurements of cytosolic Ca2+ ([Ca2+]c) responses have involved the use of different Ca2+ probes including ectopically expressed aequorin (a Ca2+-sensitive photoprotein), the fluorescent dye fura-2-dextran and the radioisotope 45Ca2+. The aequorin method (J. Cell Sci. 110:2845–2853, 1997) offers nonperturbing, real-time measurement of cytosolic free Ca2+ in suspensions of cells, but the low levels of light emission preclude measurements on individual cells. Fura-2 imaging (Cell Calcium 22:65–74, 1997; Eur. J. Cell Biol. 58:172–181, 1992; Biochem. J. 332:541–548, 1998; BMC Cell Biol. 6:13, 2005) has the advantage of allowing Ca2+ responses to be observed in individual cells so that the subcellular localisation of the response and differences amongst individual cells can be observed. However data collection is more labour intensive, much smaller numbers of cells are sampled, the cells are unavoidably damaged physically during loading and the time resolution (s) is much less than that provided by the aequorin method (ms). 45Ca2+ uptake assays (Cell Biol. Int. Rep. 2:71–79, 1978; J. Cell Biol. 112:103–110, 1991) allow measurement of Ca2+ influx from the medium by cell suspensions with a time resolution of the order of seconds. Radioactive Ca2+ uptake measurements are unsullied by but equally do not provide information about Ca2+ efflux, intracellular Ca2+ release or sequestration or changes in cytosolic free Ca2+ levels. less

关键词： Cell And Tissue Culture Cell Lysis Electroporation Fluorescence Microscopy Co-precipitation Chromatography programming language Dictyostelium Dictyostelium discoideum Saccharomyces cerevisiae Micrococcus luteus cAMP Calcium Folic acid Aequorin 45Ca2+ Fura-2-dextran

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EST Databases and Web Tools for EST Projects

EST Databases and Web Tools for EST Projects

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作者： Yao-Qing Shen Emmet O’Brien Liisa Koski B. Franz Lang Gertraud Burger

This chapter outlines key considerations for constructing and implementing an EST database. Instead of showing the technological details step by step, emphasis is put on the design of an EST database suited to the specific needs of EST projects and how to choose the most suitable tools. Using TBestDB as an example, we illustrate the essential factors to be considered for database construction and the steps for data population and annotation. This process employs technologies such as PostgreSQL, Perl, and PHP to build the database and interface, and tools such as AutoFACT for data processing and annotation. We discuss these in comparison to other available technologies and tools, and explain the reasons for our choices. less

关键词： Statistical Calculation Sequence Annotation Multiple Sequence Alignment Database Management System programming language GenBank Homo sapiens data processing annotation Web interface EST database design data submission

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