Multiplexed Massively Parallel SELEX for Characterization of Human Transcription Factor Binding Specificities
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Screening of a Clinically and Biochemically Diagnosed SOD Patient Using Exome Sequencing: a Case Report with a Mutations/Variations Analysis Approach
The Egyptian Journal of Medical Human Genetics (2016) 17, 131–136 HOSTED BY Ain Shams University The Egyptian Journal of Medical Human Genetics www.ejmhg.eg.net www.sciencedirect.com CASE REPORT Screening of a clinically and biochemically diagnosed SOD patient using exome sequencing: A case report with a mutations/variations analysis approach Mohamad-Reza Aghanoori a,b,1, Ghazaleh Mohammadzadeh Shahriary c,2, Mahdi Safarpour d,3, Ahmad Ebrahimi d,* a Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran b Research and Development Division, RoyaBioGene Co., Tehran, Iran c Department of Genetics, Shahid Chamran University of Ahvaz, Ahvaz, Iran d Cellular and Molecular Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran Received 12 May 2015; accepted 15 June 2015 Available online 22 July 2015 KEYWORDS Abstract Background: Sulfite oxidase deficiency (SOD) is a rare neurometabolic inherited disor- Sulfite oxidase deficiency; der causing severe delay in developmental stages and premature death. The disease follows an auto- Case report; somal recessive pattern of inheritance and causes deficiency in the activity of sulfite oxidase, an Exome sequencing enzyme that normally catalyzes conversion of sulfite to sulfate. Aim of the study: SOD is an underdiagnosed disorder and its diagnosis can be difficult in young infants as early clinical features and neuroimaging changes may imitate some common diseases. Since the prognosis of the disease is poor, using exome sequencing as a powerful and efficient strat- egy for identifying the genes underlying rare mendelian disorders can provide important knowledge about early diagnosis, disease mechanisms, biological pathways, and potential therapeutic targets. -
Comparative Transcriptomics of Primary Cells in Vertebrates
Edinburgh Research Explorer Comparative transcriptomics of primary cells in vertebrates Citation for published version: Alam, T, Agrawal, S, Severin, J, Young, R, Andersson, R, Amer, E, Hasegawa, A, Lizio, M, Ramilowski, J, Abugessaisa, I, Ishizu, Y, Noma, S, Tarui, H, Taylor, MS, Lassmann, T, Itoh, M, Kasukawa, T, Kawaji, H, Marchionni, L, Sheng, G, Forrest, ARR, Khachigian, LM, Hayashizaki, Y, Carninci, P & De Hoon, M 2020, 'Comparative transcriptomics of primary cells in vertebrates', Genome Research. https://doi.org/10.1101/gr.255679.119 Digital Object Identifier (DOI): 10.1101/gr.255679.119 Link: Link to publication record in Edinburgh Research Explorer Document Version: Peer reviewed version Published In: Genome Research Publisher Rights Statement: is article, published inGenome Research, is avail-able under a Creative Commons License (Attribution 4.0 Internatio General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 30. Sep. 2021 1 1 Comparative transcriptomics of primary cells in vertebrates 2 Tanvir Alam1, Saumya Agrawal2, Jessica Severin2, Robert S. Young3,4, Robin Andersson5, Erik 3 Arner2, Akira Hasegawa2, Marina Lizio2, Jordan Ramilowski2, Imad Abugessaisa2, Yuri Ishizu6, 4 Shohei Noma2, Hiroshi Tarui7, Martin S. -
Homotypic Clusters of Transcription Factor Binding Sites Are a Key Component of Human Promoters and Enhancers
Downloaded from genome.cshlp.org on October 4, 2021 - Published by Cold Spring Harbor Laboratory Press Research Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers Valer Gotea,1 Axel Visel,2,3 John M. Westlund,4 Marcelo A. Nobrega,4 Len A. Pennacchio,2,3 and Ivan Ovcharenko1,5 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA; 2Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; 3United States Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA; 4Department of Human Genetics, University of Chicago, Chicago, Illinois 60637, USA Clustering of multiple transcription factor binding sites (TFBSs) for the same transcription factor (TF) is a common feature of cis-regulatory modules in invertebrate animals, but the occurrence of such homotypic clusters of TFBSs (HCTs) in the human genome has remained largely unknown. To explore whether HCTs are also common in human and other verte- brates, we used known binding motifs for vertebrate TFs and a hidden Markov model–based approach to detect HCTs in the human, mouse, chicken, and fugu genomes, and examined their association with cis-regulatory modules. We found that evolutionarily conserved HCTs occupy nearly 2% of the human genome, with experimental evidence for individual TFs supporting their binding to predicted HCTs. More than half of the promoters of human genes contain HCTs, with a dis- tribution around the transcription start site in agreement with the experimental data from the ENCODE project. In addition, almost half of the 487 experimentally validated developmental enhancers contain them as well—a number more than 25-fold larger than expected by chance. -
Application of Genomic Technologies to Study Infertility Nicholas Rui Yuan Ho Washington University in St
Washington University in St. Louis Washington University Open Scholarship Arts & Sciences Electronic Theses and Dissertations Arts & Sciences Spring 5-15-2016 Application of Genomic Technologies to Study Infertility Nicholas Rui Yuan Ho Washington University in St. Louis Follow this and additional works at: https://openscholarship.wustl.edu/art_sci_etds Part of the Bioinformatics Commons, Genetics Commons, and the Molecular Biology Commons Recommended Citation Yuan Ho, Nicholas Rui, "Application of Genomic Technologies to Study Infertility" (2016). Arts & Sciences Electronic Theses and Dissertations. 786. https://openscholarship.wustl.edu/art_sci_etds/786 This Dissertation is brought to you for free and open access by the Arts & Sciences at Washington University Open Scholarship. It has been accepted for inclusion in Arts & Sciences Electronic Theses and Dissertations by an authorized administrator of Washington University Open Scholarship. For more information, please contact [email protected]. WASHINGTON UNIVERSITY IN ST. LOUIS Division of Biology and Biomedical Sciences Computational and Systems Biology Dissertation Examination Committee: Donald Conrad, Chair Barak Cohen Joseph Dougherty John Edwards Liang Ma Application of Genomic Technologies to Study Infertility by Nicholas Rui Yuan Ho A dissertation presented to the Graduate School of Arts & Sciences of Washington University in partial fulfillment of the requirements for the degree of Doctor of Philosophy May 2016 St. Louis, Missouri © 2016, Nicholas Rui Yuan Ho Table of -
Screening of a Clinically and Biochemically Diagnosed SOD Patient Using Exome Sequencing: a Case Report with a Mutations/Variations Analysis Approach
The Egyptian Journal of Medical Human Genetics (2016) 17, 131–136 HOSTED BY Ain Shams University The Egyptian Journal of Medical Human Genetics www.ejmhg.eg.net www.sciencedirect.com CASE REPORT Screening of a clinically and biochemically diagnosed SOD patient using exome sequencing: A case report with a mutations/variations analysis approach Mohamad-Reza Aghanoori a,b,1, Ghazaleh Mohammadzadeh Shahriary c,2, Mahdi Safarpour d,3, Ahmad Ebrahimi d,* a Department of Medical Genetics, Shiraz University of Medical Sciences, Shiraz, Iran b Research and Development Division, RoyaBioGene Co., Tehran, Iran c Department of Genetics, Shahid Chamran University of Ahvaz, Ahvaz, Iran d Cellular and Molecular Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran Received 12 May 2015; accepted 15 June 2015 Available online 22 July 2015 KEYWORDS Abstract Background: Sulfite oxidase deficiency (SOD) is a rare neurometabolic inherited disor- Sulfite oxidase deficiency; der causing severe delay in developmental stages and premature death. The disease follows an auto- Case report; somal recessive pattern of inheritance and causes deficiency in the activity of sulfite oxidase, an Exome sequencing enzyme that normally catalyzes conversion of sulfite to sulfate. Aim of the study: SOD is an underdiagnosed disorder and its diagnosis can be difficult in young infants as early clinical features and neuroimaging changes may imitate some common diseases. Since the prognosis of the disease is poor, using exome sequencing as a powerful and efficient strat- egy for identifying the genes underlying rare mendelian disorders can provide important knowledge about early diagnosis, disease mechanisms, biological pathways, and potential therapeutic targets. -
Bioinformatics Analysis of Hereditary Disease Gene Set to Identify Key Modulators of Myocardial Remodeling During Heart Regeneration in Zebrafish
EPiC Series in Computing Volume 70, 2020, Pages 226{237 Proceedings of the 12th International Conference on Bioinformatics and Computational Biology Bioinformatics analysis of hereditary disease gene set to identify key modulators of myocardial remodeling during heart regeneration in zebrafish Lawrence Yu-Min Liu1,2, Zih-Yin Lai1, Min-Hsuan Lin1, Yu Shih3 and Yung-Jen Chuang1 1 Department of Medical Science & Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 30013, Taiwan 2 Division of Cardiology, Department of Internal Medicine, Hsinchu Mackay Memorial Hospital, Hsinchu, 30071, Taiwan 3 Interdisciplinary Program of Life Science, National Tsing Hua University, Hsinchu, 30013, Taiwan [email protected], [email protected], [email protected], [email protected], [email protected] Abstract Unlike mammals, adult zebrafish hearts retain a remarkable capacity to regenerate after injury. Since regeneration shares many common molecular pathways with embryonic development, we investigated myocardial remodeling genes and pathways by performing a comparative transcriptomic analysis of zebrafish heart regeneration using a set of known human hereditary heart disease genes related to myocardial hypertrophy during development. We cross-matched human hypertrophic cardiomyopathy-associated genes with a time-course microarray dataset of adult zebrafish heart regeneration. Genes in the expression profiles that were highly elevated in the early phases of myocardial repair and remodeling after injury in zebrafish were identified. These genes were further analyzed with web-based bioinformatics tools to construct a regulatory network revealing potential transcription factors and their upstream receptors. In silico functional analysis of these genes showed that they are involved in cardiomyocyte proliferation and differentiation, angiogenesis, and inflammation-related pathways. -
Prokineticin 2 Signaling: Genetic Regulation and Preclinical Assessment in Rodent Models of Parkinsonism Jie Luo Iowa State University
Iowa State University Capstones, Theses and Graduate Theses and Dissertations Dissertations 2018 Prokineticin 2 signaling: Genetic regulation and preclinical assessment in rodent models of Parkinsonism Jie Luo Iowa State University Follow this and additional works at: https://lib.dr.iastate.edu/etd Part of the Toxicology Commons Recommended Citation Luo, Jie, "Prokineticin 2 signaling: Genetic regulation and preclinical assessment in rodent models of Parkinsonism" (2018). Graduate Theses and Dissertations. 17254. https://lib.dr.iastate.edu/etd/17254 This Dissertation is brought to you for free and open access by the Iowa State University Capstones, Theses and Dissertations at Iowa State University Digital Repository. It has been accepted for inclusion in Graduate Theses and Dissertations by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Prokineticin 2 signaling: Genetic regulation and preclinical assessment in rodent models of Parkinsonism by Jie Luo A dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Major: Toxicology Program of Study Committee: Anumantha Kanthasamy, Co-major Professor Arthi Kanthasamy, Co-major Professor Mark Ackermann Cathy Miller Thimmasettappa Thippeswamy The student author, whose presentation of the scholarship herein was approved by the program of study committee, is solely responsible for the content of this dissertation. The Graduate College will ensure this dissertation is globally accessible and will not permit alterations after a degree is conferred. Iowa State University Ames, Iowa 2018 Copyright © Jie Luo, 2018. All rights reserved. ii DEDICATION To God, my dear mother Leanne, and my girlfriend Haiyang iii TABLE OF CONTENTS Page ACKNOWLEDGMENTS ................................................................................................. -
Comparative Transcriptomics of Primary Cells in Vertebrates
Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Research Comparative transcriptomics of primary cells in vertebrates Tanvir Alam,1 Saumya Agrawal,2 Jessica Severin,2 Robert S. Young,3,4 Robin Andersson,5 Erik Arner,2 Akira Hasegawa,2 Marina Lizio,2 Jordan A. Ramilowski,2 Imad Abugessaisa,2 Yuri Ishizu,6,13,14 Shohei Noma,2 Hiroshi Tarui,6,13 Martin S. Taylor,4 Timo Lassmann,2,7 Masayoshi Itoh,8 Takeya Kasukawa,2 Hideya Kawaji,2,8 Luigi Marchionni,9 Guojun Sheng,10 Alistair R.R. Forrest,2,11 Levon M. Khachigian,12 Yoshihide Hayashizaki,8 Piero Carninci,2 and Michiel J.L. de Hoon2 1College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar; 2RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; 3Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, United Kingdom; 4MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom; 5The Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark; 6RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Yokohama 230-0045, Japan; 7Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia; 8RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan; 9Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA; 10International Research Center for -
University of California, San Diego
UC San Diego UC San Diego Electronic Theses and Dissertations Title Cell type specific gene expression : profiling and targeting Permalink https://escholarship.org/uc/item/36m3m5n3 Author Nathanson, Jason Lawrence Publication Date 2008 Peer reviewed|Thesis/dissertation eScholarship.org Powered by the California Digital Library University of California UNIVERSITY OF CALIFORNIA, SAN DIEGO Cell type specific gene expression: profiling and targeting A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Bioengineering by Jason Lawrence Nathanson Committee in charge: Professor Lanping Amy Sung, Chair Professor Edward M Callaway, Co-Chair Professor Fred H Gage Professor Vivian Hook Professor Xiaohua Huang Professor Gabriel A Silva 2008 Copyright Jason Nathanson, 2008 All rights reserved. The Dissertation of Jason Lawrence Nathanson is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Co-chair Chair University of California, San Diego 2008 iii DEDICATION I dedicate this dissertation in recognition of the untiring support and encouragement from family and friends. I am especially grateful to my parents for their support and love from the beginning of my days, to my mom’s parents for their unwavering financial and inspirational support of my undergraduate and graduate school endeavors, to my dad’s parents for their love and hugs, to my brothers and sisters for their laughter and encouragement, and to Noah for his tolerance of my late hours and grouchy moods. My appreciation also goes to all my teachers and co-workers for their guidance, patience and goodwill. iv TABLE OF CONTENTS Signature Page……………………………………………………………... -
Identification of Novel Regulatory Genes in Acetaminophen
IDENTIFICATION OF NOVEL REGULATORY GENES IN ACETAMINOPHEN INDUCED HEPATOCYTE TOXICITY BY A GENOME-WIDE CRISPR/CAS9 SCREEN A THESIS IN Cell Biology and Biophysics and Bioinformatics Presented to the Faculty of the University of Missouri-Kansas City in partial fulfillment of the requirements for the degree DOCTOR OF PHILOSOPHY By KATHERINE ANNE SHORTT B.S, Indiana University, Bloomington, 2011 M.S, University of Missouri, Kansas City, 2014 Kansas City, Missouri 2018 © 2018 Katherine Shortt All Rights Reserved IDENTIFICATION OF NOVEL REGULATORY GENES IN ACETAMINOPHEN INDUCED HEPATOCYTE TOXICITY BY A GENOME-WIDE CRISPR/CAS9 SCREEN Katherine Anne Shortt, Candidate for the Doctor of Philosophy degree, University of Missouri-Kansas City, 2018 ABSTRACT Acetaminophen (APAP) is a commonly used analgesic responsible for over 56,000 overdose-related emergency room visits annually. A long asymptomatic period and limited treatment options result in a high rate of liver failure, generally resulting in either organ transplant or mortality. The underlying molecular mechanisms of injury are not well understood and effective therapy is limited. Identification of previously unknown genetic risk factors would provide new mechanistic insights and new therapeutic targets for APAP induced hepatocyte toxicity or liver injury. This study used a genome-wide CRISPR/Cas9 screen to evaluate genes that are protective against or cause susceptibility to APAP-induced liver injury. HuH7 human hepatocellular carcinoma cells containing CRISPR/Cas9 gene knockouts were treated with 15mM APAP for 30 minutes to 4 days. A gene expression profile was developed based on the 1) top screening hits, 2) overlap with gene expression data of APAP overdosed human patients, and 3) biological interpretation including assessment of known and suspected iii APAP-associated genes and their therapeutic potential, predicted affected biological pathways, and functionally validated candidate genes. -
Gundurao2013.Pdf
This thesis has been submitted in fulfilment of the requirements for a postgraduate degree (e.g. PhD, MPhil, DClinPsychol) at the University of Edinburgh. Please note the following terms and conditions of use: • This work is protected by copyright and other intellectual property rights, which are retained by the thesis author, unless otherwise stated. • A copy can be downloaded for personal non-commercial research or study, without prior permission or charge. • This thesis cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author. • The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author. • When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given. Systematic analysis of protein‐protein interactions of oncogenic human papillomavirus Ramya M. Gundurao A thesis presented for the degree of Doctor of Philosophy, The University of Edinburgh February 2013 Division of Pathway Medicine College of Medicine and Veterinary Medicine The University of Edinburgh DECLARATION I hereby declare that this thesis and the work presented in it are my own. I confirm that: This work was done wholly or mainly while in candidature for a research degree at this University. Where any part of this thesis has previously been submitted for a degree or any other qualification at this University or any other institution, this has been clearly stated. Where I have consulted the published work of others, this is always clearly attributed. Where I have quoted from the work of others, the source is always given. -
Tfcat: the Curated Catalog of Mouse and Human Transcription Factors
Open Access Software2009FultonetVolume al. 10, Issue 3, Article R29 TFCat: the curated catalog of mouse and human transcription factors Debra L Fulton*, Saravanan Sundararajan†, Gwenael Badis‡, Timothy R Hughes‡, Wyeth W Wasserman¤*, Jared C Roach¤§ and Rob Sladek¤† Addresses: *Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics - Child and Family Research Institute, University of British Columbia, West 28th Avenue, Vancouver, V5Z 4H4, Canada. †Departments of Medicine and Human Genetics, McGill University and Genome Quebec Innovation Centre, Dr. Penfield Avenue, Montreal, H3A 1A4, Canada. ‡Banting and Best Department of Medical Research, University of Toronto, College Street, Toronto, M5S 3E1, Canada. §Center for Developmental Therapeutics, Seattle Children's Research Institute, Olive Way, Seattle, 98101, USA. ¤ These authors contributed equally to this work. Correspondence: Rob Sladek. Email: [email protected] Published: 12 March 2009 Received: 5 December 2008 Revised: 26 February 2009 Genome Biology 2009, 10:R29 (doi:10.1186/gb-2009-10-3-r29) Accepted: 12 March 2009 The electronic version of this article is the complete one and can be found online at http://genomebiology.com/2009/10/3/R29 © 2009 Fulton et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Transcription<p>TFCatof the scientific is a factorcatalog literature</p> catalog of mouse and human transcription factors based on a reliable core collection of annotations obtained by expert review Abstract Unravelling regulatory programs governed by transcription factors (TFs) is fundamental to understanding biological systems.