University of California, Santa Cruz Genome Browser ENCODE
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ENCODE Genome-Wide Data on the UCSC Genome Browser Melissa Cline ENCODE Data Coordination Center (DCC) UC Santa Cruz
ENCODE Genome-Wide Data on the UCSC Genome Browser Melissa Cline ENCODE Data Coordination Center (DCC) UC Santa Cruz http://encodeproject.org Slides at http://genome-preview.ucsc.edu/ What is ENCODE? • International consortium project with the goal of cataloguing the functional regions of the human genome GTTTGCCATCTTTTG! CTGCTCTAGGGAATC" CAGCAGCTGTCACCA" TGTAAACAAGCCCAG" GCTAGACCAGTTACC" CTCATCATCTTAGCT" GATAGCCAGCCAGCC" ACCACAGGCATGAGT" • A gold mine of experimental data for independent researchers with available disk space ENCODE covers diverse regulatory processes ENCODE experiments are planned for integrative analysis Example of ENCODE data Genes Dnase HS Chromatin Marks Chromatin State Transcription Factor Binding Transcription RNA Binding Translation ENCODE tracks on the UCSC Genome Browser ENCODE tracks marked with the NHGRI helix There are currently 2061 ENCODE experiments at the ENCODE DCC How to find the data you want Finding ENCODE tracks the hard way A better way to find ENCODE tracks Finding ENCODE metadata descriptions Visualizing: Genome Browser tricks that every ENCODE user should know Turning ENCODE subtracks and views on and off Peaks Signal View on/off Subtrack on/off Right-click to the subtrack display menu Subtrack Drag and Drop Sessions: the easy way to save and share your work Downloading data with less pain 1. Via the Downloads button on the track details page 2. Via the File Selection tool Publishing: the ENCODE data release policy Every ENCODE subtrack has a “Restricted Until” date Key points of the ENCODE data release policy • Anyone is free to download and analyze data. • One cannot submit publications involving ENCODE data unless – the data has been at the ENCODE DCC for at least nine months, or – the data producers have published on the data, or – the data producers have granted permission to publish. -
No Evidence for Recent Selection at FOXP2 Among Diverse Human Populations
Article No Evidence for Recent Selection at FOXP2 among Diverse Human Populations Graphical Abstract Authors Elizabeth Grace Atkinson, Amanda Jane Audesse, Julia Adela Palacios, Dean Michael Bobo, Ashley Elizabeth Webb, Sohini Ramachandran, Brenna Mariah Henn Correspondence [email protected] (E.G.A.), [email protected] (B.M.H.) In Brief An in-depth examination of diverse sets of human genomes argues against a recent selective evolutionary sweep of FOXP2, a gene that was believed to be critical for speech evolution in early hominins. Highlights d No support for positive selection at FOXP2 in large genomic datasets d Sample composition and genomic scale significantly affect selection scans d An intronic ROI within FOXP2 is expressed in human brain cells and cortical tissue d This ROI contains a large amount of constrained, human- specific polymorphisms Atkinson et al., 2018, Cell 174, 1424–1435 September 6, 2018 ª 2018 Elsevier Inc. https://doi.org/10.1016/j.cell.2018.06.048 Article No Evidence for Recent Selection at FOXP2 among Diverse Human Populations Elizabeth Grace Atkinson,1,8,9,10,* Amanda Jane Audesse,2,3 Julia Adela Palacios,4,5 Dean Michael Bobo,1 Ashley Elizabeth Webb,2,6 Sohini Ramachandran,4 and Brenna Mariah Henn1,7,* 1Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA 2Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA 3Neuroscience Graduate Program, Brown University, Providence, RI 02912, USA 4Department of Ecology and Evolutionary -
ENCODE Regions Identification of Higher-Order Functional Domains in the Human
Downloaded from www.genome.org on August 14, 2007 Identification of higher-order functional domains in the human ENCODE regions Robert E. Thurman, Nathan Day, William S. Noble and John A. Stamatoyannopoulos Genome Res. 2007 17: 917-927 Access the most recent version at doi:10.1101/gr.6081407 Supplementary "Supplemental Research Data" data http://www.genome.org/cgi/content/full/17/6/917/DC1 References This article cites 45 articles, 17 of which can be accessed free at: http://www.genome.org/cgi/content/full/17/6/917#References Article cited in: http://www.genome.org/cgi/content/full/17/6/917#otherarticles Open Access Freely available online through the Genome Research Open Access option. Email alerting Receive free email alerts when new articles cite this article - sign up in the box at the service top right corner of the article or click here Notes To subscribe to Genome Research go to: http://www.genome.org/subscriptions/ © 2007 Cold Spring Harbor Laboratory Press Downloaded from www.genome.org on August 14, 2007 Methods Identification of higher-order functional domains in the human ENCODE regions Robert E. Thurman,1,2 Nathan Day,3 William S. Noble,2,3 and John A. Stamatoyannopoulos2,4 1Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; 2Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; 3Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA It has long been posited that human and other large genomes are organized into higher-order (i.e., greater than gene-sized) functional domains. -
Developing and Implementing an Institute-Wide Data Sharing Policy Stephanie OM Dyke and Tim JP Hubbard*
Dyke and Hubbard Genome Medicine 2011, 3:60 http://genomemedicine.com/content/3/9/60 CORRESPONDENCE Developing and implementing an institute-wide data sharing policy Stephanie OM Dyke and Tim JP Hubbard* Abstract HapMap Project [7], also decided to follow HGP prac- tices and to share data publicly as a resource for the The Wellcome Trust Sanger Institute has a strong research community before academic publications des- reputation for prepublication data sharing as a result crib ing analyses of the data sets had been prepared of its policy of rapid release of genome sequence (referred to as prepublication data sharing). data and particularly through its contribution to the Following the success of the first phase of the HGP [8] Human Genome Project. The practicalities of broad and of these other projects, the principles of rapid data data sharing remain largely uncharted, especially to release were reaffirmed and endorsed more widely at a cover the wide range of data types currently produced meeting of genomics funders, scientists, public archives by genomic studies and to adequately address and publishers in Fort Lauderdale in 2003 [9]. Meanwhile, ethical issues. This paper describes the processes the Organisation for Economic Co-operation and and challenges involved in implementing a data Develop ment (OECD) Committee on Scientific and sharing policy on an institute-wide scale. This includes Tech nology Policy had established a working group on questions of governance, practical aspects of applying issues of access to research information [10,11], which principles to diverse experimental contexts, building led to a Declaration on access to research data from enabling systems and infrastructure, incentives and public funding [12], and later to a set of OECD guidelines collaborative issues. -
Databases/Resources on the Web
Jon K. Lærdahl, Structural Bioinforma�cs Databases/Resources on the web Jon K. Lærdahl [email protected] Jon K. Lærdahl, A lot of biological databases Structural Bioinforma�cs available on the web... MetaBase, the database of biological bioinforma�cs.ca – links directory databases (1801 entries) (620 databases) -‐ h�p://metadatabase.org -‐ h�p://bioinforma�cs.ca/links_directory Jon K. Lærdahl, Structural Bioinforma�cs btw, the bioinforma�cs.ca links directory is an excellent resource bioinforma�cs.ca – links directory h�p://bioinforma�cs.ca/links_directory Currently 1459 tools 620 databases 164 “resources” The problem is not to find a tool or database, but to know what is “gold” and what is “junk” Jon K. Lærdahl, Some important centres for Structural Bioinforma�cs bioinforma�cs Na�onal Center for Biotechnology Informa�on (NCBI) – part of the US Na�onal Library of Medicine (NLM), a branch of the Na�onal Ins�tutes of Health – located in Bethesda, Maryland European Bioinforma�cs Ins�tute (EMBL-‐EBI) – part of part of European Molecular Biology Laboratory (EMBL) – located in Hinxton, Cambridgeshire, UK Jon K. Lærdahl, NCBI databases Structural Bioinforma�cs Provided the GenBank DNA sequence database since 1992 Online Mendelian Inheritance in Man (OMIM) -‐ known diseases with a gene�c component and links to genes – started early 1960s as a book – online version, OMIM, since 1987 – on the WWW by NCBI in 1995 – currently >22,000 entries (14,400 genes) EST -‐ nucleo�de database subset that contains only Expressed Sequence Tag -
The UCSC Genome Browser Database: 2021 Update Jairo Navarro Gonzalez 1,*, Ann S
D1046–D1057 Nucleic Acids Research, 2021, Vol. 49, Database issue Published online 22 November 2020 doi: 10.1093/nar/gkaa1070 The UCSC Genome Browser database: 2021 update Jairo Navarro Gonzalez 1,*, Ann S. Zweig1, Matthew L. Speir1, Daniel Schmelter1, Kate R. Rosenbloom1, Brian J. Raney1, Conner C. Powell1, Luis R. Nassar1, Nathan D. Maulding1, Christopher M. Lee 1, Brian T. Lee 1,AngieS.Hinrichs1, Alastair C. Fyfe1, Jason D. Fernandes1, Mark Diekhans 1, Hiram Clawson1, Jonathan Casper1, Anna Benet-Pages` 1,2, Galt P. Barber1, David Haussler1,3, Robert M. Kuhn1, Maximilian Haeussler1 and W. James Kent1 Downloaded from https://academic.oup.com/nar/article/49/D1/D1046/5998393 by guest on 27 September 2021 1Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA, 2Medical Genetics Center (MGZ), Munich, Germany and 3Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA Received September 21, 2020; Revised October 19, 2020; Editorial Decision October 20, 2020; Accepted November 18, 2020 ABSTRACT pires to quickly incorporate and contextualize vast amounts of genomic information. For more than two decades, the UCSC Genome Apart from incorporating data from researchers and con- Browser database (https://genome.ucsc.edu)has sortia, the Browser also provides tools available for users to provided high-quality genomics data visualization view and compare their own data with ease. Custom tracks and genome annotations to the research community. allow users to quickly view a dataset, and track hubs allow As the field of genomics grows and more data be- users to extensively organize their data and share it privately come available, new modes of display are required using a URL. -
Estimating the Number of Unseen Variants in the Human Genome
Estimating the number of unseen variants in the human genome Iuliana Ionita-Laza1, Christoph Lange, and Nan M. Laird Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 02115b; Edited by Peter J. Bickel, University of California, Berkeley, CA, and approved January 7, 2009 (received for review August 8, 2008) The different genetic variation discovery projects (The SNP Consor- not use. Specifically, if a new volume by Shakespeare were to be tium, the International HapMap Project, the 1000 Genomes Project, discovered, how many new words would we expect to see? Efron etc.) aim to identify as much as possible of the underlying genetic and Thisted (7) used a Gamma-Poisson model to address this variation in various human populations. The question we address in question. We adapt the approach in Efron and Thisted to the this article is how many new variants are yet to be found. This is an problem of predicting the number of genetic variants yet to be instance of the species problem in ecology, where the goal is to esti- identified in future studies. The method also allows calculation of mate the number of species in a closed population. We use a para- the number of individuals required to be sequenced in order to metric beta-binomial model that allows us to calculate the expected detect all (or a fraction of) the variants with a given minimum fre- number of new variants with a desired minimum frequency to be quency. In the following sections we develop the method and show discovered in a new dataset of individuals of a specified size. -
The UCSC Genome Browser Database: Update 2011 Pauline A
D876–D882 Nucleic Acids Research, 2011, Vol. 39, Database issue Published online 18 October 2010 doi:10.1093/nar/gkq963 The UCSC Genome Browser database: update 2011 Pauline A. Fujita1,*, Brooke Rhead1, Ann S. Zweig1, Angie S. Hinrichs1, Donna Karolchik1, Melissa S. Cline1, Mary Goldman1, Galt P. Barber1, Hiram Clawson1, Antonio Coelho1, Mark Diekhans1, Timothy R. Dreszer1, Belinda M. Giardine2, Rachel A. Harte1, Jennifer Hillman-Jackson1, Fan Hsu1, Vanessa Kirkup1, Robert M. Kuhn1, Katrina Learned1, Chin H. Li1, Laurence R. Meyer1, Andy Pohl1,3, Brian J. Raney1, Kate R. Rosenbloom1, Kayla E. Smith1, David Haussler1,4 and W. James Kent1 1Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz Downloaded from (UCSC), Santa Cruz, CA 95064, 2Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA, 3Centre for Genomic Regulation (CRG), Barcelona, Spain and 4Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA Received September 15, 2010; Accepted September 30, 2010 nar.oxfordjournals.org ABSTRACT differs among species, with recent assemblies of the human The University of California, Santa Cruz Genome genome being the most richly annotated. The Genome Browser (http://genome.ucsc.edu) offers online Browser contains mapping and sequencing annotation tracks describing assembly, gap and GC percent details access to a database of genomic sequence and at Health Sciences Center Library on February 4, 2011 annotation data for a wide variety of organisms. for all assemblies. Most organisms also have tracks con- taining alignments of RefSeq genes (3,4), mRNAs and The Browser also has many tools for visualizing, ESTs from GenBank (5) as well as gene and gene predic- comparing and analyzing both publicly available tion tracks such as Ensembl Genes (6). -
Genetic Analyses in a Bonobo (Pan Paniscus) with Arrhythmogenic Right Ventricular Cardiomyopathy Received: 19 September 2017 Patrícia B
www.nature.com/scientificreports OPEN Genetic analyses in a bonobo (Pan paniscus) with arrhythmogenic right ventricular cardiomyopathy Received: 19 September 2017 Patrícia B. S. Celestino-Soper1, Ty C. Lynnes1, Lili Zhang1, Karen Ouyang1, Samuel Wann2, Accepted: 21 February 2018 Victoria L. Clyde2 & Matteo Vatta1,3 Published: xx xx xxxx Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a disorder that may lead to sudden death and can afect humans and other primates. In 2012, the alpha male bonobo of the Milwaukee County Zoo died suddenly and histologic evaluation found features of ARVC. This study sought to discover a possible genetic cause for ARVC in this individual. We sequenced our subject’s DNA to search for deleterious variants in genes involved in cardiovascular disorders. Variants found were annotated according to the human genome, following currently available classifcation used for human diseases. Sequencing from the DNA of an unrelated unafected bonobo was also used for prediction of pathogenicity. Twenty-four variants of uncertain clinical signifcance (VUSs) but no pathogenic variants were found in the proband studied. Further familial, functional, and bonobo population studies are needed to determine if any of the VUSs or a combination of the VUSs found may be associated with the clinical fndings. Future genotype-phenotype establishment will be benefcial for the appropriate care of the captive zoo bonobo population world-wide as well as conservation of the bobono species in its native habitat. Cardiovascular disease is a leading cause of death for both human and non-human primates, who share similar genomes and many environmental and lifestyle characteristics1. However, while humans most ofen die due to coronary artery disease (CAD), non-human primates living in captivity are more ofen afected by hypertensive cardiomyopathy1. -
The ENCODE Project
RESEARCH HIGHLIGHTS GENOMICS The ENCODE project The second, genome-wide phase of a particular product (for instance, a protein ENCODE-defined functional element in at the Encyclopedia of DNA Elements or noncoding RNA) or has a consistent bio- least one examined cell type; an even larger (ENCODE) project is being reported. chemical property (for instance, being bound fraction (99%) lies nearby such an element The function of most of the human by protein or having a particular biochemical (within 1.7 kilobases). An examination of genome is unknown. Protein-coding genes mark). previously identified disease-associated account for only a small fraction (about 3%) The laboratories in the ENCODE Project single-nucleotide polymorphisms shows that of the total genome sequence; most func- Consortium have developed and applied a they are enriched in ENCODE-annotated tional genomic sequences are likely to have huge range of sequencing-based techniques regions, suggesting hypotheses for functional regulatory roles. Understanding human to map functional elements across the consequences of single-nucleotide polymor- gene organization and regulation and their genome. To put it succinctly, the ENCODE phisms that can be further tested. impact on normal and disease phenotypes project has mapped chromatin state and The data generated by ENCODE are vast requires that functional elements be mapped structure, three-dimensional genome organi- and can be only very briefly summarized and annotated across the genome. This is the zation, DNA methylation, transcription fac- here. The collected ENCODE papers may goal of the ENCODE project. tor binding, RNA transcription and protein be examined at http://www.encodeproject. The initial 5-year pilot phase of the proj- expression genome wide. -
The ENCODE (Encyclopedia of S DNA Elements) Project
GGENESENES IN INAACTIONCTION VIEWPOINT ECTION The ENCODE (ENCyclopedia Of S DNA Elements) Project PECIAL The ENCODE Project Consortium*. S The ENCyclopedia Of DNA Elements (ENCODE) Project aims to identify all functional approaches, such as cDNA-cloning efforts elements in the human genome sequence. The pilot phase of the Project is focused on (4, 5) and chip-based transcriptome analyses a specified 30 megabases (È1%) of the human genome sequence and is organized as (6, 7), have revealed the existence of many an international consortium of computational and laboratory-based scientists transcribed sequences of unknown function. working to develop and apply high-throughput approaches for detecting all sequence As a reflection of this complexity, about 5% elements that confer biological function. The results of this pilot phase will guide of the human genome is evolutionarily future efforts to analyze the entire human genome. conserved with respect to rodent genomic sequences, and therefore is inferred to be With the complete human genome sequence namics; undoubtedly, additional, yet-to-be- functionally important (8, 9). Yet only about now in hand (1–3), we face the enormous defined types of functional sequences will one-third of the sequence under such selec- challenge of interpreting it and learning how also need to be included. tion is predicted to encode proteins (1, 2). to use that information to understand the To illustrate the magnitude of the chal- Our collective knowledge about putative biology of human health and disease. The lenge involved, it only needs to be pointed out functional, noncoding elements, which repre- ENCyclopedia Of DNA Elements (ENCODE) that an inventory of the best-defined func- sent the majority of the remaining functional Project is predicated on the belief that a tional components in the human genome— sequences in the human genome, is remark- comprehensive catalog of the structural and the protein-coding sequences—is still incom- ably underdeveloped at the present time. -
Cgb − a Unix Shell Program to Create Custom Instances of the Ucsc Genome Browser
CGB − A UNIX SHELL PROGRAM TO CREATE CUSTOM INSTANCES OF THE UCSC GENOME BROWSER Vincenzo Forgetta1* & Ken Dewar1 1Department of Human Genetics, McGill University, Montreal, Quebec, Canada. *Corresponding author: Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste-Catherine Road, H-465 (Pavilion H), Montreal, Québec, H3T 1E2, Tel: +1 (514) 340-8222 ext.3982, Fax: +1 (514) 340-7564, Email: [email protected] Keywords: UCSC Genome Browser, genomics, custom mirror procedure. Abstract The UCSC Genome Browser is a popular tool for the exploration and analysis of reference genomes. Mirrors of the UCSC Genome Browser and its contents exist at multiple geographic locations, and this mirror procedure has been modified to support genome sequences not maintained by UCSC and generated by individual researchers. While straightforward, this procedure is lengthy and tedious and would benefit from automation, especially when processing many genome sequences. We present a Unix shell program that facilitates the creation of custom instances of the UCSC Genome Browser for genome sequences not being maintained by UCSC. It automates many steps of the browser creation process, provides password protection for each browser instance, and automates the creation of basic annotation tracks. As an example we generate a custom UCSC Genome Browser for a bacterial genome obtained from a massively parallel sequencing platform. Introduction In the past, large institutions sequenced de novo the genome of organisms such as human (Lander et al., 2001), mouse (Waterston et al., 2002) and fly (Adams et al., 2000), and bioinformatics tools were created to provide the scientific research community with access to analyzing these reference genome resources.