Mammalian genome : official journal of the International Mammalian Genome Society最新文献_第10页

GeneWeaver: finding consilience in heterogeneous cross-species functional genomics data. GeneWeaver:发现异质跨物种功能基因组数据的一致性。

IF 2.5

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2015-10-01 Epub Date: 2015-06-20 DOI: 10.1007/s00335-015-9575-x

Jason A Bubier, Charles A Phillips, Michael A Langston, Erich J Baker, Elissa J Chesler

{"title":"GeneWeaver: finding consilience in heterogeneous cross-species functional genomics data.","authors":"Jason A Bubier, Charles A Phillips, Michael A Langston, Erich J Baker, Elissa J Chesler","doi":"10.1007/s00335-015-9575-x","DOIUrl":"https://doi.org/10.1007/s00335-015-9575-x","url":null,"abstract":"A persistent challenge lies in the interpretation of consensus and discord from functional genomics experimentation. Harmonizing and analyzing this data will enable investigators to discover relations of many genes to many diseases, and from many phenotypes and experimental paradigms to many diseases through their genomic substrates. The GeneWeaver.org system provides a platform for cross-species integration and interrogation of heterogeneous curated and experimentally derived functional genomics data. GeneWeaver enables researchers to store, share, analyze, and compare results of their own genome-wide functional genomics experiments in an environment containing rich companion data obtained from major curated repositories, including the Mouse Genome Database and other model organism databases, along with derived data from highly specialized resources, publications, and user submissions. The data, largely consisting of gene sets and putative biological networks, are mapped onto one another through gene identifiers and homology across species. A versatile suite of interactive tools enables investigators to perform a variety of set analysis operations to find consilience among these often noisy experimental results. Fast algorithms enable real-time analysis of large queries. Specific applications include prioritizing candidate genes for quantitative trait loci, identifying biologically valid mouse models and phenotypic assays for human disease, finding the common biological substrates of related diseases, classifying experiments and the biological concepts they represent from empirical data, and applying patterns of genomic evidence to implicate novel genes in disease. These results illustrate an alternative to strict emphasis on replicability, whereby researchers classify experimental results to identify the conditions that lead to their similarity. ","PeriodicalId":412165,"journal":{"name":"Mammalian genome : official journal of the International Mammalian Genome Society","volume":" ","pages":"556-66"},"PeriodicalIF":2.5,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00335-015-9575-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33278865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 9

Talking welfare: the importance of a common language. 谈福利：共同语言的重要性。

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2015-10-01 Epub Date: 2015-08-19 DOI: 10.1007/s00335-015-9591-x

James Bussell, Sara E Wells

引用次数: 0

Application of comparative biology in GO functional annotation: the mouse model. 比较生物学在氧化石墨烯功能注释中的应用:小鼠模型。

IF 2.5

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2015-10-01 Epub Date: 2015-07-04 DOI: 10.1007/s00335-015-9580-0

Harold J Drabkin, Karen R Christie, Mary E Dolan, David P Hill, Li Ni, Dmitry Sitnikov, Judith A Blake

{"title":"Application of comparative biology in GO functional annotation: the mouse model.","authors":"Harold J Drabkin, Karen R Christie, Mary E Dolan, David P Hill, Li Ni, Dmitry Sitnikov, Judith A Blake","doi":"10.1007/s00335-015-9580-0","DOIUrl":"https://doi.org/10.1007/s00335-015-9580-0","url":null,"abstract":"The Gene Ontology (GO) is an important component of modern biological knowledge representation with great utility for computational analysis of genomic and genetic data. The Gene Ontology Consortium (GOC) consists of a large team of contributors including curation teams from most model organism database groups as well as curation teams focused on representation of data relevant to specific human diseases. Key to the generation of consistent and comprehensive annotations is the development and use of shared standards and measures of curation quality. The GOC engages all contributors to work to a defined standard of curation that is presented here in the context of annotation of genes in the laboratory mouse. Comprehensive understanding of the origin, epistemology, and coverage of GO annotations is essential for most effective use of GO resources. Here the application of comparative approaches to capturing functional data in the mouse system is described. ","PeriodicalId":412165,"journal":{"name":"Mammalian genome : official journal of the International Mammalian Genome Society","volume":" ","pages":"574-83"},"PeriodicalIF":2.5,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00335-015-9580-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33877863","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 11

Beyond knockouts: the International Knockout Mouse Consortium delivers modular and evolving tools for investigating mammalian genes. 除敲除外:国际敲除小鼠联盟为研究哺乳动物基因提供模块化和不断发展的工具。

IF 2.5

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2015-10-01 Epub Date: 2015-09-04 DOI: 10.1007/s00335-015-9598-3

B Rosen, J Schick, W Wurst

{"title":"Beyond knockouts: the International Knockout Mouse Consortium delivers modular and evolving tools for investigating mammalian genes.","authors":"B Rosen, J Schick, W Wurst","doi":"10.1007/s00335-015-9598-3","DOIUrl":"https://doi.org/10.1007/s00335-015-9598-3","url":null,"abstract":"The International Knockout Mouse Consortium (IKMC; http://www.mousephenotype.org ) has generated mutations in almost every protein-coding mouse gene and is completing the companion Cre driver resource to expand tissue-specific conditional mutagenesis. Accordingly, the IKMC has carried out high-throughput gene trapping and targeting producing conditional mutations in murine embryonic stem cells in more than 18,500 genes, from which at least 4900 mutant mouse lines have been established to date. This resource is currently being upgraded with more powerful tools, such as visualization and manipulation cassettes that can be easily introduced into IKMC alleles for multifaceted functional studies. In addition, we discuss how existing IKMC products can be used in combination with CRISPR technology to accelerate genome engineering projects. All information and materials from this extraordinary biological resource together with coordinated phenotyping efforts can be retrieved at www.mousephenotype.org . The comprehensive IKMC knockout resource in combination with an extensive set of modular gene cassettes will continue to enhance functional gene annotation in the future and solidify its impact on biomedical research. ","PeriodicalId":412165,"journal":{"name":"Mammalian genome : official journal of the International Mammalian Genome Society","volume":" ","pages":"456-66"},"PeriodicalIF":2.5,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00335-015-9598-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33978761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 31

The International Mouse Strain Resource (IMSR): cataloging worldwide mouse and ES cell line resources. 国际小鼠品系资源(IMSR):编目全球小鼠和胚胎干细胞系资源。

IF 2.5

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2015-10-01 Epub Date: 2015-09-15 DOI: 10.1007/s00335-015-9600-0

Janan T Eppig, Howie Motenko, Joel E Richardson, Beverly Richards-Smith, Cynthia L Smith

引用次数: 52

The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes. 小鼠基因组计划：一个近交实验室小鼠品系基因组库。

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2015-10-01 Epub Date: 2015-06-30 DOI: 10.1007/s00335-015-9579-6

David J Adams, Anthony G Doran, Jingtao Lilue, Thomas M Keane

{"title":"The Mouse Genomes Project: a repository of inbred laboratory mouse strain genomes.","authors":"David J Adams, Anthony G Doran, Jingtao Lilue, Thomas M Keane","doi":"10.1007/s00335-015-9579-6","DOIUrl":"10.1007/s00335-015-9579-6","url":null,"abstract":"The Mouse Genomes Project was initiated in 2009 with the goal of using next-generation sequencing technologies to catalogue molecular variation in the common laboratory mouse strains, and a selected set of wild-derived inbred strains. The initial sequencing and survey of sequence variation in 17 inbred strains was completed in 2011 and included comprehensive catalogue of single nucleotide polymorphisms, short insertion/deletions, larger structural variants including their fine scale architecture and landscape of transposable element variation, and genomic sites subject to post-transcriptional alteration of RNA. From this beginning, the resource has expanded significantly to include 36 fully sequenced inbred laboratory mouse strains, a refined and updated data processing pipeline, and new variation querying and data visualisation tools which are available on the project's website ( http://www.sanger.ac.uk/resources/mouse/genomes/ ). The focus of the project is now the completion of de novo assembled chromosome sequences and strain-specific gene structures for the core strains. We discuss how the assembled chromosomes will power comparative analysis, data access tools and future directions of mouse genetics. ","PeriodicalId":412165,"journal":{"name":"Mammalian genome : official journal of the International Mammalian Genome Society","volume":" ","pages":"403-12"},"PeriodicalIF":0.0,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33305694","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Introduction to Mammalian Genome special issue: Informatics and Integrative Genomics--Part 2. 介绍哺乳动物基因组特刊：信息学和整合基因组学-第2部分。

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2015-10-01 DOI: 10.1007/s00335-015-9604-9

Ann-Marie Mallon

引用次数: 0

Visual annotation display (VLAD): a tool for finding functional themes in lists of genes. 可视化注释显示(VLAD):在基因列表中寻找功能主题的工具。

IF 2.5

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2015-10-01 Epub Date: 2015-06-06 DOI: 10.1007/s00335-015-9570-2

Joel E Richardson, Carol J Bult

{"title":"Visual annotation display (VLAD): a tool for finding functional themes in lists of genes.","authors":"Joel E Richardson, Carol J Bult","doi":"10.1007/s00335-015-9570-2","DOIUrl":"https://doi.org/10.1007/s00335-015-9570-2","url":null,"abstract":"Experiments that employ genome scale technology platforms frequently result in lists of tens to thousands of genes with potential significance to a specific biological process or disease. Searching for biologically relevant connections among the genes or gene products in these lists is a common data analysis task. We have implemented a software application for uncovering functional themes in sets of genes based on their annotations to bio-ontologies, such as the gene ontology and the mammalian phenotype ontology. The application, called VisuaL Annotation Display (VLAD), performs a statistical analysis to test for the enrichment of ontology terms in a set of genes submitted by a researcher. The results for each analysis using VLAD includes a table of ontology terms, sorted in decreasing order of significance. Each row contains the term, statistics such as the number of annotated terms, the p value, etc., and the symbols of annotated genes. An accompanying graphical display shows portions of the ontology hierarchy, where node sizes are scaled based on p values. Although numerous ontology term enrichment programs already exist, VLAD is unique in that it allows users to upload their own annotation files and ontologies for customized term enrichment analyses, supports the analysis of multiple gene sets at once, provides interfaces to customize graphical output, and is tightly integrated with functional and biological details about mouse genes in the Mouse Genome Informatics (MGI) database. VLAD is available as a web-based application from the MGI web site (http://proto.informatics.jax.org/prototypes/vlad/).","PeriodicalId":412165,"journal":{"name":"Mammalian genome : official journal of the International Mammalian Genome Society","volume":" ","pages":"567-73"},"PeriodicalIF":2.5,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00335-015-9570-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33244642","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 42

Disease insights through cross-species phenotype comparisons. 通过跨物种表型比较了解疾病。

IF 2.5

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2015-10-01 Epub Date: 2015-06-20 DOI: 10.1007/s00335-015-9577-8

Melissa A Haendel, Nicole Vasilevsky, Matthew Brush, Harry S Hochheiser, Julius Jacobsen, Anika Oellrich, Christopher J Mungall, Nicole Washington, Sebastian Köhler, Suzanna E Lewis, Peter N Robinson, Damian Smedley

{"title":"Disease insights through cross-species phenotype comparisons.","authors":"Melissa A Haendel, Nicole Vasilevsky, Matthew Brush, Harry S Hochheiser, Julius Jacobsen, Anika Oellrich, Christopher J Mungall, Nicole Washington, Sebastian Köhler, Suzanna E Lewis, Peter N Robinson, Damian Smedley","doi":"10.1007/s00335-015-9577-8","DOIUrl":"https://doi.org/10.1007/s00335-015-9577-8","url":null,"abstract":"New sequencing technologies have ushered in a new era for diagnosis and discovery of new causative mutations for rare diseases. However, the sheer numbers of candidate variants that require interpretation in an exome or genomic analysis are still a challenging prospect. A powerful approach is the comparison of the patient's set of phenotypes (phenotypic profile) to known phenotypic profiles caused by mutations in orthologous genes associated with these variants. The most abundant source of relevant data for this task is available through the efforts of the Mouse Genome Informatics group and the International Mouse Phenotyping Consortium. In this review, we highlight the challenges in comparing human clinical phenotypes with mouse phenotypes and some of the solutions that have been developed by members of the Monarch Initiative. These tools allow the identification of mouse models for known disease-gene associations that may otherwise have been overlooked as well as candidate genes may be prioritized for novel associations. The culmination of these efforts is the Exomiser software package that allows clinical researchers to analyse patient exomes in the context of variant frequency and predicted pathogenicity as well the phenotypic similarity of the patient to any given candidate orthologous gene. ","PeriodicalId":412165,"journal":{"name":"Mammalian genome : official journal of the International Mammalian Genome Society","volume":" ","pages":"548-55"},"PeriodicalIF":2.5,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s00335-015-9577-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33278866","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 26

Current strategies for mutation detection in phenotype-driven screens utilising next generation sequencing. 利用下一代测序在表型驱动筛选中进行突变检测的当前策略。

Mammalian genome : official journal of the International Mammalian Genome Society Pub Date : 2015-10-01 Epub Date: 2015-10-08 DOI: 10.1007/s00335-015-9603-x

Michelle M Simon, Eva Marie Y Moresco, Katherine R Bull, Saumya Kumar, Ann-Marie Mallon, Bruce Beutler, Paul K Potter

{"title":"Current strategies for mutation detection in phenotype-driven screens utilising next generation sequencing.","authors":"Michelle M Simon, Eva Marie Y Moresco, Katherine R Bull, Saumya Kumar, Ann-Marie Mallon, Bruce Beutler, Paul K Potter","doi":"10.1007/s00335-015-9603-x","DOIUrl":"10.1007/s00335-015-9603-x","url":null,"abstract":"Mutagenesis-based screens in mice are a powerful discovery platform to identify novel genes or gene functions associated with disease phenotypes. An N-ethyl-N-nitrosourea (ENU) mutagenesis screen induces single nucleotide variants randomly in the mouse genome. Subsequent phenotyping of mutant and wildtype mice enables the identification of mutated pathways resulting in phenotypes associated with a particular ENU lesion. This unbiased approach to gene discovery conducts the phenotyping with no prior knowledge of the functional mutations. Before the advent of affordable next generation sequencing (NGS), ENU variant identification was a limiting step in gene characterization, akin to 'finding a needle in a haystack'. The emergence of a reliable reference genome alongside advances in NGS has propelled ENU mutation discovery from an arduous, time-consuming exercise to an effective and rapid form of mutation discovery. This has permitted large mouse facilities worldwide to use ENU for novel mutation discovery in a high-throughput manner, helping to accelerate basic science at the mechanistic level. Here, we describe three different strategies used to identify ENU variants from NGS data and some of the subsequent steps for mutation characterisation. ","PeriodicalId":412165,"journal":{"name":"Mammalian genome : official journal of the International Mammalian Genome Society","volume":" ","pages":"486-500"},"PeriodicalIF":0.0,"publicationDate":"2015-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4602060/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34243454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0