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检索条件"主题词=Data Visualization Tools"

共 34 条记录，以下是11-20 订阅

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Using PLINK for Genome-Wide Association Studies (GWAS) and data Analysis

Using PLINK for Genome-Wide Association Studies (GWAS) and D...

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作者： Miguel E. Rentería Adrian Cortes Sarah E. Medland

Within this chapter we introduce the basic PLINK functions for reading in data, applying quality control, and running association analyses. Three worked examples are provided to illustrate: data management and assessment of population substructure, association analysis of a quantitative trait, and qualitative or case–control association analyses. less

关键词： data visualization tools Genotyping data analysis Homo sapiens Population stratification data management Multidimensional scaling PLINK Quantitative trait Genetic association Binomial trait

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Mass Spectrometry-Based Proteomics

Mass Spectrometry-Based Proteomics

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作者： Marcos Rafael Di Falco

Proteomics is the large-scale analysis of proteins rendered possible by modern mass spectrometry analysis methods capable of identifying thousands of peptides/proteins in a fast high-throughput manner. Here I describe protocols for the preparation of fungal culture protein samples for mass spectrometry-based proteomics analysis including protein sample cleanup, proteolytic digestion, LC-MS/MS separation, and database search protein identification. less

关键词： Liquid Chromatography-tandem Mass Spectrometry database Search Proteomics Mass Spectrometry HPLC Nanoflow High-performance Liquid Chromatography Electrospray Ionization (ESI) Bottom-up Proteomics Tandem Mass Spectrometry Peptide Identification De Novo Sequencing data visualization tools Liquid Chromatography-mass Spectrometry In-gel digestion In-solution digestion Fungal proteome Microcapillary column packing

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The Bio-Analytic Resource for Plant Biology

The Bio-Analytic Resource for Plant Biology

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作者： Jamie Waese Nicholas J. Provart

Bioinformatic tools have become part of the way plant researchers undertake investigations. Large data sets encompassing genomes, transcriptomes, proteomes, epigenomes, and other “-omes” that have been generated in the past decade may be easily accessed with such tools, such that hypotheses may be generated at the click of a mouse. In this chapter, we’ll cover the use of bioinformatic tools available at the Bio-Analytic Resource for Plant Biology at http://*** for exploring gene expression and coexpression patterns, undertaking promoter analyses, performing functional classification enrichment analyses for sets of genes, and examining protein-protein interactions. We also touch on some newer bioinformatic tools that allow integration of data from several sources for improved hypothesis generation, both for Arabidopsis and translationally. Most of the data sets come from Arabidopsis, but useful BAR tools for other species will be mentioned where appropriate. less

关键词： Transcriptomics Proteomics Functional Genomics Cytoscape Yeast Two-hybrid Assay Position-Specific Scoring Matrices data visualization tools Gene Expression Profiling Genome Analysis Arabidopsis thaliana Populus (cottonwood) Medicago truncatula Solanum lycopersicum Zea mays Oryza sativa Physcomitrella patens Solanum tuberosum Bioinformatics Promoter analysis Protein-protein interactions In silico Subcellular localization eFP Coexpression Functional classification Hypothesis generation Translational biology

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Holistic and Affordable Analyses of MicroRNA Expression Profiles Using Tagged cDNA Libraries and a Multiplex Sequencing Strategy

Holistic and Affordable Analyses of MicroRNA Expression Prof...

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作者： Patrick P. Weil Yan Jaszczyszyn Anne Baroin-Tourancheau Jan Postberg Laurence Amar

Small and long noncoding RNAs (ncRNAs) are key regulators of gene expression. Variations in ncRNA expression patterns can consequently affect the control of many cellular processes. Not just since 2006, when Andrew Z Fire and Craig C Mello were jointly awarded The Nobel Prize in Physiology or Medicine for their discovery of RNA interference, great efforts were undertaken to unleash the biomedical applicability of small noncoding RNAs, in particular microRNAs. With the technological evolution of massive parallel sequencing technologies over the last years, which now are available for an increasing number of scientists, there is a demand for comprehensible and efficient workflows reliable even for unique and valuable clinical specimens. Here we describe a highly reproducible low-cost protocol for analyses of miRNA expression patterns using tagged cDNA libraries and a multiplex sequencing strategy following an Illumina-like protocol. This protocol easily allows the identification of expression differences from samples of tissues of 1–2 mm3 and fluids of 50–200 μL. We further provide entry points into useful computational biology applications, whose target groups explicitly involve non-bioinformaticians. less

关键词： RNA Interference Cell And Tissue Culture Electrophoresis PCR data visualization tools DNA Ligation microRNA miRNome Multiplex sequencing

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data Mining and Computational Modeling of High-Throughput Screening datasets

Data Mining and Computational Modeling of High-Throughput Sc...

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作者： Sean Ekins Alex M. Clark Krishna Dole Kellan Gregory Andrew M. Mcnutt Anna Coulon Spektor Charlie Weatherall Nadia K. Litterman Barry A. Bunin

We are now seeing the benefit of investments made over the last decade in high-throughput screening (HTS) that is resulting in large structure activity datasets entering public and open databases such as ChEMBL and PubChem. The growth of academic HTS screening centers and the increasing move to academia for early stage drug discovery suggests a great need for the informatics tools and methods to mine such data and learn from it. Collaborative Drug Discovery, Inc. (CDD) has developed a number of tools for storing, mining, securely and selectively sharing, as well as learning from such HTS data. We present a new web based data mining and visualization module directly within the CDD Vault platform for high-throughput drug discovery data that makes use of a novel technology stack following modern reactive design principles. We also describe CDD Models within the CDD Vault platform that enables researchers to share models, share predictions from models, and create models from distributed, heterogeneous data. Our system is built on top of the Collaborative Drug Discovery Vault Activity and Registration data repository ecosystem which allows users to manipulate and visualize thousands of molecules in real time. This can be performed in any browser on any platform. In this chapter we present examples of its use with public datasets in CDD Vault. Such approaches can complement other cheminformatics tools, whether open source or commercial, in providing approaches for data mining and modeling of HTS data. less

关键词： data Mining High-throughput Screening Machine Learning Statistical Calculation Reporter Assay Decision Tree data visualization tools Homo sapiens Mus musculus Mycobacterium tuberculosis Ebola virus visualization ADME Bayesian models CDD models CDD vault Collaborative database

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Single-Cell Single-Molecule Pull-Down (sc-SiMPull) for Detection of Protein Complexes from Embryonic Lysates

Single-Cell Single-Molecule Pull-Down (sc-SiMPull) for Detec...

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作者： Naomi Stolpner Daniel J. Dickinson

Mapping how proteins form complexes and change binding partners is central to understanding cell signaling. Bulk biochemistry can provide a summary of what complexes are present in a cell, but information about the diversity of individual protein complexes is lost. Here, we describe single-cell, single-molecule pull-down (sc-SiMPull), a TIRFTotal internal reflection fluorescence microscopy (TIRF) microscopy-based coimmunoprecipitation method, to visualize thousands of individual proteins, their binding partners, and protein complex stoichiometry directly from single-cell lysate. By iterating sc-SiMPull over time, temporal dynamics of protein complexes in response to signaling can be constructed. less

关键词： TIRF Microscopy Co-immunoprecipitation Soft Lithography Spin Coating Electrophoresis Sonication Biopsy Passivation HPLC MATLAB data visualization tools Fluorescence Labeling PCR Dissection Pull-down Assay data analysis Caenorhabditis elegans Escherichia coli Microfluidics Biochemistry Development Single cell TIRF Single molecule Cell polarity Anti-HaloTag

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Structure-Based Virtual Screening for Novel Ligands

Structure-Based Virtual Screening for Novel Ligands

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作者： William R. Pitt Mark D. Calmiano Boris Kroeplien Richard D. Taylor James P. Turner Michael A. King

Computational searches for novel ligands for a given protein binding site have become ubiquitous in the pharmaceutical industry, and are potentially equally useful in helping identify small-molecule tools for biology. Here we describe the steps needed to carry out a high-throughput docking (HTD) or three-dimensional (3D) pharmacophore virtual screen starting with a model of the target protein’s structure. The advice given is, in most cases, software independent but some tips are provided which apply only to certain popular programs. Useful work can be carried out using free programs on a modest workstation. Of course, any resultant “hits” remain in the virtual world until they are experimentally tested. less

关键词： Virtual Screening Molecular Modeling Protein Structure Analysis Homology Modeling Molecular Dynamics Simulation Molecular Docking X-ray Crystallography data visualization tools AutoDock Docking Method Computational chemistry Pharmacophores Docking

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Analysis of Volatile Organic Compounds in Exhaled Breath by Gas Chromatography-Mass Spectrometry Combined with Chemometric Analysis

Analysis of Volatile Organic Compounds in Exhaled Breath by ...

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作者： Jan W. Dallinga Agnieszka Smolinska Frederik-Jan Schooten

Analysis of exhaled breath samples reveals the presence of many volatile organic compounds (VOCs). The VOC composition of the breath, the so-called breath profile, contains a variety of information including the health status and condition of the organism that produced the sample. Therefore, breath profiling can be used in diagnosing and monitoring disease and other characteristics of the organism, such as phenotype, diet, and exercise. Among various techniques available for breath analysis, GC-MS provides the most extensive information with regard to the qualitative and quantitative presence of VOCs in breath. less

关键词： Gas Chromatography (GC) Gas Chromatography-mass Spectrometry Statistical Calculation data visualization tools Principal Component Analysis Chromatography Mass Spectrometry data analysis Homo sapiens Chemometrics Breath analysis Volatile organic compounds Breath sampling Breathomics Correlation-optimized warping

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Interactive Alternative Splicing Analysis of Human Stem Cells Using

Interactive Alternative Splicing Analysis of Human Stem Cell...

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作者： Nuno Saraiva-Agostinho Nuno Luís Barbosa-Morais

Alternative splicing (AS) generates functionally distinct transcripts and is involved in multiple cellular processes, including stem cell differentiation. Several epithelial-to-mesenchymal transition-related splicing factors have also been associated with pluripotency. Concomitantly with the interest in studying AS in stem cell biology, the advent of next-generation sequencing of RNA (RNA-seq) has increased the public availability of transcriptomic data and enabled genome-wide AS studies. To facilitate performing such analyses in large publicly available or user-provided transcriptomics datasets, the psichomics R package provides an easy-to-use interface and efficient data visualization tools for AS quantification and integrative analyses of AS and gene expression data. psichomics is employed herein to study AS changes between human stem cells and fibroblasts, based on dimensionality reduction, and median- and variance-based differential AS and gene expression analyses. Putative RNA-binding protein regulators involved in those alterations are then identified based on correlation analyses in large cohorts of human tissue transcriptomes. We identified several alterations, both novel and previously reported, in alternative splicing events and in the expression of their candidate regulators that are associated with stem cell differentiation into fibroblasts. less

关键词： RNA-seq Principal Component Analysis Gene Expression Analysis Splicing Model Analysis Transcriptomics data visualization tools Statistical Calculation Genome Assembly Homo sapiens Stemness psichomics Integrative analyses

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Requirements, Features, and Performance of High Content Screening Platforms

Requirements, Features, and Performance of High Content Scre...

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作者： Albert H. Gough Paul A. Johnston

High content screening (HCS) platforms integrate fluorescence microscopy with image analysis algorithms and informatics to automate cell analysis. The initial applications of HCS to secondary screening in drug discovery have spread throughout the discovery pipeline, and now into the expanding research field of systems cell biology, in which new manipulation tools enable the use of large scale screens to understand cellular pathways, and cell functions. In this chapter we discuss the requirements for HCS and the systems that have been designed to meet these application needs. The number of HCS systems available in the market place, and the range of features available, has grown considerably in the past 2 yr. Of the two general optical designs, the confocal systems have dominated the high-throughput HCS market, whereas the more cost effective wide-field systems have dominated all other market segments, and have a much larger market share. The majority of available systems have been optimized for fixed cell applications; however, there is growing interest in live cell kinetic assays, and four systems have successfully penetrated this application area. The breadth of applications for these systems continues to expand, especially with the integration of new technologies. New applications, improved software, better data visualization tools, and new detection methods such as multispectral imaging and fluorescence lifetime are predicted to drive the development of future HCS platforms. less

关键词： Microscopy Fluorescence Microscopy Image Analysis data visualization tools Multispectral Imaging Automation imaging high-throughput fluorescence drug discovery high content screening systems cell biology confocal

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