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Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser
2005
BMC Bioinformatics
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Statistical Viewer is an add-on package to the open-source Ensembl Genome Browser and Annotation System that displays disease study-specific linkage and/or association data as 2 dimensional plots in new ...
To resolve Association and Fine mapping data plots, a "Detailed Statistic View" plot corresponding to the "Detailed View" may be displayed underneath. ...
to make Statistic View available through the public site. ...
doi:10.1186/1471-2105-6-95
pmid:15826305
pmcid:PMC1087836
fatcat:mpbejkdbmnaj5g7upboxoflfwu
Analysis of Complex Disease Association and Linkage Studies Using the University of California Santa Cruz Genome Browser
2009
Circulation: Cardiovascular Genetics
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The online-only Data Supplement is available at http://circgenetics.ahajournals.org/cgi/content/full/2/2/199/DC1. ...
Disclosures Dr Furey is a partner in the Genome Browser Authors partnership, which licenses the UCSC Genome Browser software to profit entities. ...
Sources of Funding This study was supported by the Duke Institute for Genome Sciences and Policy and National Institutes of Health grants HL073389 (Hauser), MH059528 (Hauser) and HL73042 (Goldschmidt, ...
doi:10.1161/circgenetics.108.843946
pmid:20031585
pmcid:PMC2798134
fatcat:mgy7kusauzdabhcesfnmiusqge
GenomeGraphs: integrated genomic data visualization with R
2009
BMC Bioinformatics
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GenomeGraphs is a flexible and extensible software package which can be used to visualize a multitude of genomic datasets within the statistical programming environment R. ...
We developed GenomeGraphs, as an add-on software package for the statistical programming environment R, to facilitate integrated visualization of genomic datasets. ...
The package has been tested and run on OS X, Windows, and a variety of Linux systems. ...
doi:10.1186/1471-2105-10-2
pmid:19123956
pmcid:PMC2629762
fatcat:vk4rd4vyy5airap55dckjyysuq
Exploring the Landscape of the Genome
[chapter]
2010
Msphere
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The comprehensive range of information presented in tools such as the UCSC genome browser and Ensembl enables integrated queries of data that are otherwise reserved to the most skilled computational biologists ...
While at a micro level, genome annotation can help to describe the full complexity of gene regulation, variation, and transcript diversity. ...
Although there are many ways to access genomic information in an integrated manner, there are two primary tools that are the acknowledged leaders in the field, the UCSC human genome browser (1) and ENSEMBL ...
doi:10.1007/978-1-60327-367-1_2
pmid:20238074
fatcat:d37ygpseorcgnjfhsvtvbv4tey
A survey of tools for variant analysis of next-generation genome sequencing data
2013
Briefings in Bioinformatics
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While whole-exome and, in the near future, whole-genome sequencing are becoming commodities, data analysis still poses significant challenges and led to the development of a plethora of tools supporting ...
We report an overview of the functionality, features and specific requirements of the individual tools. ...
Acknowledgements We thank the reviewers for their numerous constructive suggestions, which helped us to considerably improve the article. ...
doi:10.1093/bib/bbs086
pmid:23341494
pmcid:PMC3956068
fatcat:zcunpg3i7bfrvhm5dixp6r6ofq
Genome Expression Pathway Analysis Tool – Analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context
2007
BMC Bioinformatics
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We provide an integration of statistical methods for data import and data analysis together with a biological interpretation for subsets of probes or single probes on the chip. ...
GEPAT offers no linear work flow, but allows the usage of any subset of probes and samples as a start for a new data analysis. ...
JE was funded by the IZKF of the University of Würzburg and by the BMBF project FUNCRYPTA (FKZ 0313838B). MW wants to thank P. Seibel for help with programming issues, S. ...
doi:10.1186/1471-2105-8-179
pmid:17543125
pmcid:PMC1896182
fatcat:bvmudnp27jbmzbwugigreq4y7m
easyGWAS: A Cloud-Based Platform for Comparing the Results of Genome-Wide Association Studies
2016
The Plant Cell
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The easyGWAS tool supports multiple species, the uploading of private genotype data and summary statistics of existing GWAS, as well as advanced methods for comparing GWAS results across different experiments ...
Other advantages that result from the integration of multiple GWAS are the ability to replicate GWAS signals and to increase statistical power to detect such signals through meta-analyses. ...
the uploading of summary statistics of GWAS obtained from third-party tools; (4) it provides a variety of different methods to correct for multiple hypothesis testing; and, most importantly, (5) it integrates ...
doi:10.1105/tpc.16.00551
pmid:27986896
pmcid:PMC5304348
fatcat:fbq5cwbwv5hovblsc5hkb5k7dq
Growing and cultivating the forest genomics database, TreeGenes
2018
Database: The Journal of Biological Databases and Curation
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This focus was paired with the development of tools to enable comparative genomics and data visualization. ...
This migration enabled developments focused on data exchange, data transfer and improved analytical capacity, as well as providing TreeGenes the opportunity to communicate with the following partner databases ...
Acknowledgements We would like to thank the Computational Biology Core within the Institute of Systems Genomics at the University of Connecticut and The High Performance Computing Facility at the UConn ...
doi:10.1093/database/bay084
pmid:30239664
pmcid:PMC6146132
fatcat:o5a5wj5ylvdkdncttoebsk3ni4
Online Resources for SNP Analysis: A Review and Route Map
2007
Molecular Biotechnology
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The major online single nucleotide polymorphism (SNP) databases freely available as research tools for genetic analysis are explained, reviewed, and compared. ...
the most appropriate data for the research needs of clinical genetics and population genetics research. ...
Ensembl is one of the principal genome data repositories with extensive databases and search tools stemming from the integral role of The Sanger Centre and EMBL in HGP and the position of Ensembl in providing ...
doi:10.1385/mb:35:1:65
pmid:17401150
fatcat:3aifzadxlnd65pvn4zqxeas774
Analyzing Proteomes and Protein Function Using Graphical Comparative Analysis of Tandem Mass Spectrometry Results
2006
Molecular & Cellular Proteomics
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Currently available applications are typically designed for displaying proteins and posttranslational modifications from the point of view of the mass spectrometrist and are not versatile enough to allow ...
Our system, Bioinformatic Graphical Comparative Analysis Tools (BIGCAT), allows sophisticated analysis of tandem mass spectrometry results in a biologically intuitive format and provides a solution to ...
The annotation page provides the user with the annotations for the protein as well as links to outside annotation services including Ensembl, RefSeq, Gene Ontology, Swiss-Prot, Saccharomyces Genome Database ...
doi:10.1074/mcp.t500027-mcp200
pmid:16707483
fatcat:orqf4pvq4rfvpgczejx3kaxofy
Visualizing the drug target landscape
2010
Drug Discovery Today
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A retrospective on how the application of data integration and visualisation has been used to connect disparate information sources into a drug-discovery focused, decision making environment. ...
Acknowledgements The authors acknowledge the guidance of Enoch Huang and substantial input from Robert Hernandez, Markella Skempri, Dave ...
Beyond predetermined content The major genome viewers (University of California Santa Cruz, or UCSC [5] ; Ensembl [6] ; and the Generic Genome Browser, or GBrowse [7] ) illustrate the benefits of systems ...
doi:10.1016/j.drudis.2009.09.011
pmid:19840866
fatcat:csd4hsaokjgbjjbq4azwdnf24q
RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse
2021
biorxiv/medrxiv
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Comparisons to other gene regulatory datasets show that the RefSeqFE dataset includes a wider range of feature types representing more areas of biology, but it is comparatively smaller and subject to data ...
The data have multiple uses for basic functional discovery, bioinformatics studies, genetic variant interpretation, as known positive controls for epigenomic data evaluation, and as reference standards ...
details and data clarifications. ...
doi:10.1101/gr.275819.121
pmid:34876495
pmcid:PMC8744684
fatcat:dichersxxfcdfijtp33emabx3u
Leveraging the new with the old: providing a framework for the integration of historic microarray studies with next generation sequencing
2014
BMC Bioinformatics
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A suite of custom software tools have been developed to rapidly integrate, explore, discover and validate molecular profiling data from the NGS modalities of Whole Exome Sequencing (WES) and RNA-seq with ...
In this regard, necessity dictated a need to utilize and leverage the many years of historical microarray data with new NGS approaches. ...
Acknowledgements Appreciation and thanks to Mr. Daniel Pollock for his programming assistance. ...
doi:10.1186/1471-2105-15-s11-s3
pmid:25350881
pmcid:PMC4251047
fatcat:5pxiqqrjvrbmdoyj7uujznkl4u
Visualizing the drug target landscape
2012
Drug Discovery Today
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A retrospective on how the application of data integration and visualisation has been used to connect disparate information sources into a drug-discovery focused, decision making environment. ...
Acknowledgements The authors acknowledge the guidance of Enoch Huang and substantial input from Robert Hernandez, Markella Skempri, Dave ...
Beyond predetermined content The major genome viewers (University of California Santa Cruz, or UCSC [5] ; Ensembl [6] ; and the Generic Genome Browser, or GBrowse [7] ) illustrate the benefits of systems ...
doi:10.1016/j.drudis.2011.12.005
pmid:22178891
fatcat:qvdkemacwbaibb42sb4om6dxke
Functional Annotation of Putative Regulatory Elements at Cancer Susceptibility Loci
2014
Cancer Informatics
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Most cancer-associated genetic variants identified from genome-wide association studies (GWAS) do not obviously change protein structure, leading to the hypothesis that the associations are attributable ...
Translating genetic associations into mechanistic insights can be facilitated by knowledge of the causal regulatory variant (or variants) responsible for the statistical signal. ...
The UCSC Cancer Genome Browser currently displays a growing catalog of data, including 201 datasets from 22 TCGA (The Cancer Genome Atlas) cancers as well as data from Cancer Cell Line Encyclopedia and ...
doi:10.4137/cin.s13789
pmid:25288875
pmcid:PMC4179605
fatcat:gitz7qou3ndlpbcwznuccorrcq
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