Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser

BACKGROUND: To facilitate efficient selection and the prioritization of candidate complex disease susceptibility genes for association analysis, increasingly comprehensive annotation tools are essential to integrate, visualize and analyze vast quantities of disparate data generated by genomic screens, public human genome sequence annotation and ancillary biological databases. We have developed a plug-in package for Ensembl called "Statistical Viewer" that facilitates the analysis of genomic features and annotation in the regions of interest defined by linkage analysis. RESULTS: 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 panels in the context of Ensembl's Contig View and Cyto View pages. An enhanced upload server facilitates the upload of statistical data, as well as additional feature annotation to be displayed in DAS tracts, in the form of Excel Files. The Statistical View panel, drawn directly under the ideogram, illustrates lod score values for markers from a study of interest that are plotted against their position in base pairs. A module called "Get Map" easily converts the genetic locations of markers to genomic coordinates. The graph is placed under the corresponding ideogram features a synchronized vertical sliding selection box that is seamlessly integrated into Ensembl's Contig- and Cyto- View pages to choose the region to be displayed in Ensembl's "Overview" and "Detailed View" panels. To resolve Association and Fine mapping data plots, a "Detailed Statistic View" plot corresponding to the "Detailed View" may be displayed underneath. CONCLUSION: Features mapping to regions of linkage are accentuated when Statistic View is used in conjunction with the Distributed Annotation System (DAS) to display supplemental laboratory information such as differentially expressed disease genes in private data tracks. Statistic View is a novel and powerful visual feature that enhances Ensembl's utility as valuable resource for integrative genomic-based approaches to the identification of candidate disease susceptibility genes. At present there are no other tools that provide for the visualization of 2-dimensional plots of quantitative data scores against genomic coordinates in the context of a primary public genome annotation browser

Способы перевода аббревиатур и сокращений в области компьютерных технологий (на примере русского и немецкого языков)

Выпускная квалификационная работа 75 с., 2 главы, 42 источника. Предмет исследования: способы перевода аббревиатур и сокращений в области компьютерных технологий с немецкого языка на русский язык. Объектом исследования: аббревиатуры и сокращения, относящиеся к области компьютерных технологий. Цель работы: выявить эффективные способы перевода аббревиатур и сокращений в области компьютерных технологий с немецкого языка на русский. Результаты исследования: были сформулированы особенности перевода аббревиатур и сокращений в области компьютерных технологий Степень внедрения/апробация работы: Было опубликовано две статьи Область применения: лингвистика, языкознание, переводоведение.Graduation thesis: 75 pg., 2 chapters, 42 resources. Subject of research: translation methods of acronyms and reductions in the field of computer technology from German into Russian. Object of research: Acronyms and reductions in the field of computer technology. Purpose of research: : to identify the translation methods of acronyms and reductions in the field of computer technology from German into Russian. Results of research: The features of the translation of acronyms and reductions in the area of computer technology has been revealed. Degree of implementation /work approbation: two articles were published. Field of application: Linguistic, theory of translatio

Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser-0

<p><b>Copyright information:</b></p><p>Taken from "Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser"</p><p>BMC Bioinformatics 2005;6():95-95.</p><p>Published online 12 Apr 2005</p><p>PMCID:PMC1087836.</p><p>Copyright © 2005 Stenger et al; licensee BioMed Central Ltd.</p>aptured using SnagIt 7.0. The figure illustrates the appearance of the Statistic View panel and some of its features in the context of Contig View. It also demonstrates how the selection of a peak can enable the researcher to easily see where linkage data and other features such as potentially unstable tri-nucleotide repeats and gene expression data converge to suggest priority gene for association and sequence analysis

Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser-3

<p><b>Copyright information:</b></p><p>Taken from "Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser"</p><p>BMC Bioinformatics 2005;6():95-95.</p><p>Published online 12 Apr 2005</p><p>PMCID:PMC1087836.</p><p>Copyright © 2005 Stenger et al; licensee BioMed Central Ltd.</p

Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser-2

<p><b>Copyright information:</b></p><p>Taken from "Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser"</p><p>BMC Bioinformatics 2005;6():95-95.</p><p>Published online 12 Apr 2005</p><p>PMCID:PMC1087836.</p><p>Copyright © 2005 Stenger et al; licensee BioMed Central Ltd.</p> (part B) of three data records that define plot coordinates along with other attributes. User databases are created to allow restricted access for uploading data

Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser-1

<p><b>Copyright information:</b></p><p>Taken from "Statistical Viewer: a tool to upload and integrate linkage and association data as plots displayed within the Ensembl genome browser"</p><p>BMC Bioinformatics 2005;6():95-95.</p><p>Published online 12 Apr 2005</p><p>PMCID:PMC1087836.</p><p>Copyright © 2005 Stenger et al; licensee BioMed Central Ltd.</p>age

Genomic convergence: identifying candidate genes for Parkinson's disease by combining serial analysis of gene expression and genetic linkage

We present a multifactorial, multistep approach called genomic convergence that combines gene expression with genomic linkage analysis to identify and prioritize candidate susceptibility genes for Parkinson's disease (PD). To initiate this process, we used serial analysis of gene expression (SAGE) to identify genes expressed in two normal substantia nigras (SN) and adjacent midbrain tissue. This identified over 3700 transcripts, including the three most abundant SAGE tags, which did not correspond to any known genes or ESTs. We developed high-throughput bioinformatics methods to map the genes corresponding to these tags and identified 402 SN genes that lay within five large genomic linkage regions, previously identified in 174 multiplex PD families. These genes represent excellent candidates for PD susceptibility alleles and further genomic convergence and analyses

Mutations in the pleckstrin homology domain of dynamin 2 cause dominant intermediate Charcot-Marie-Tooth disease

Charcot-Marie-Tooth (CMT) disease is a clinically and genetically heterogeneous group of peripheral neuropathies. Different chromosomal loci have been linked with three autosomal dominant, 'intermediate' types of CMT: DI-CMTA, DI-CMTB and DI-CMTC. We refined the locus associated with DI-CMTB on chromosome 19p12-13.2 to 4.2 Mb in three unrelated families with CMT originating from Australia, Belgium and North America. After screening candidate genes, we identified unique mutations in dynamin 2 (DNM2) in all families. DNM2 belongs to the family of large GTPases and is part of the cellular fusion-fission apparatus. In transiently transfected cell lines, mutations of DNM2 substantially diminish binding of DNM2 to membranes by altering the conformation of the beta3/beta4 loop of the pleckstrin homology domain. Additionally, in the Australian and Belgian pedigrees, which carry two different mutations affecting the same amino acid, Lys558, CMT cosegregated with neutropenia, which has not previously been associated with CMT neuropathies.status: publishe