Case Report Clinical Report of a 17Q12 Microdeletion with Additionally Unreported Clinical Features
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Analysis of Gene Expression Data for Gene Ontology
ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Robert Daniel Macholan May 2011 ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION Robert Daniel Macholan Thesis Approved: Accepted: _______________________________ _______________________________ Advisor Department Chair Dr. Zhong-Hui Duan Dr. Chien-Chung Chan _______________________________ _______________________________ Committee Member Dean of the College Dr. Chien-Chung Chan Dr. Chand K. Midha _______________________________ _______________________________ Committee Member Dean of the Graduate School Dr. Yingcai Xiao Dr. George R. Newkome _______________________________ Date ii ABSTRACT A tremendous increase in genomic data has encouraged biologists to turn to bioinformatics in order to assist in its interpretation and processing. One of the present challenges that need to be overcome in order to understand this data more completely is the development of a reliable method to accurately predict the function of a protein from its genomic information. This study focuses on developing an effective algorithm for protein function prediction. The algorithm is based on proteins that have similar expression patterns. The similarity of the expression data is determined using a novel measure, the slope matrix. The slope matrix introduces a normalized method for the comparison of expression levels throughout a proteome. The algorithm is tested using real microarray gene expression data. Their functions are characterized using gene ontology annotations. The results of the case study indicate the protein function prediction algorithm developed is comparable to the prediction algorithms that are based on the annotations of homologous proteins. -
Nucleosome Positioning Signals in Genomic DNA
Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Letter Nucleosome positioning signals in genomic DNA Heather E. Peckham,1,2 Robert E. Thurman,3 Yutao Fu,1 John A. Stamatoyannopoulos,4 William Stafford Noble,4,5 Kevin Struhl,6 and Zhiping Weng1,2,7 1Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA; 2Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA; 3Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA; 4Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; 5Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA; 6Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA Although histones can form nucleosomes on virtually any genomic sequence, DNA sequences show considerable variability in their binding affinity. We have used DNA sequences of Saccharomyces cerevisiae whose nucleosome binding affinities have been experimentally determined (Yuan et al. 2005) to train a support vector machine to identify the nucleosome formation potential of any given sequence of DNA. The DNA sequences whose nucleosome formation potential are most accurately predicted are those that contain strong nucleosome forming or inhibiting signals and are found within nucleosome length stretches of genomic DNA with continuous nucleosome formation or inhibition signals. We have accurately predicted the experimentally determined nucleosome positions across a well-characterized promoter region of S. cerevisiae and identified strong periodicity within 199 center-aligned mononucleosomes studied recently (Segal et al. 2006) despite there being no periodicity information used to train the support vector machine. -
Targeted Exome Sequencing Provided Comprehensive Genetic Diagnosis of Congenital Anomalies of the Kidney and Urinary Tract
Journal of Clinical Medicine Article Targeted Exome Sequencing Provided Comprehensive Genetic Diagnosis of Congenital Anomalies of the Kidney and Urinary Tract 1,2, 3,4, 3 1,5 Yo Han Ahn y, Chung Lee y, Nayoung K. D. Kim , Eujin Park , Hee Gyung Kang 1,2,6,* , Il-Soo Ha 1,2,6, Woong-Yang Park 3,4,7 and Hae Il Cheong 1,2,6 1 Department of Pediatrics, Seoul National University College of Medicine, Seoul 03080, Korea; [email protected] (Y.H.A.); [email protected] (E.P.); [email protected] (I.-S.H.); [email protected] (H.I.C.) 2 Department of Pediatrics, Seoul National University Children’s Hospital, Seoul 03080, Korea 3 Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Korea; [email protected] (C.L.); [email protected] (N.K.D.K.); [email protected] (W.-Y.P.) 4 Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06351, Korea 5 Department of Pediatrics, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, Korea 6 Kidney Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul 03080, Korea 7 Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Korea * Correspondence: [email protected] These authors equally contributed to this article. y Received: 31 January 2020; Accepted: 8 March 2020; Published: 10 March 2020 Abstract: Congenital anomalies of the kidney and urinary tract (CAKUT) are the most common cause of chronic kidney disease in children. -
Both Sense and Antisense Strands of the LTR of the Schistosoma Mansoni Pao-Like Retrotransposon Sinbad Drive Luciferase Expression
Mol Genet Genomics DOI 10.1007/s00438-006-0181-1 ORIGINAL PAPER Both sense and antisense strands of the LTR of the Schistosoma mansoni Pao-like retrotransposon Sinbad drive luciferase expression Claudia S. Copeland · Victoria H. Mann · Paul J. Brindley Received: 20 August 2006 / Accepted: 4 October 2006 © Springer-Verlag 2006 Abstract Long terminal repeat (LTR) retrotranspo- activity in HeLa cells. The ability of the Sinbad LTR to sons, mobile genetic elements comprising substantial transcribe in both its forward and inverted orientation proportions of many eukaryotic genomes, are so represents one of few documented examples of bidirec- named for the presence of LTRs, direct repeats about tional promotor function. 250–600 bp in length Xanking the open reading frames that encode the retrotransposon enzymes and struc- Keywords Schistosome · Boudicca · Promotor · tural proteins. LTRs include promotor functions as Promoter · Bidirectional · Inverse well as other roles in retrotransposition. LTR retro- transposons, including the Gypsy-like Boudicca and the Pao/BEL-like Sinbad elements, comprise a sub- Introduction stantial proportion of the genome of the human blood Xuke, Schistosoma mansoni. In order to deduce the Eukaryotic genomes generally contain substantial capability of speciWc copies of Boudicca and Sinbad amounts of repetitive sequences, many of which repre- LTRs to function as promotors, these LTRs were sent mobile genetic elements (e.g., Lander et al. 2001; investigated analytically and experimentally. Sequence Holt et al. 2002). These mobile elements have played analysis revealed the presence of TATA boxes, canoni- fundamental roles in host genome evolution (Charles- cal polyadenylation signals, and direct inverted repeats worth et al. -
Identifying Genetic Risk Factors for Coronary Artery Angiographic Stenosis in a Genetically Diverse Population
Please do not remove this page Identifying Genetic Risk Factors for Coronary Artery Angiographic Stenosis in a Genetically Diverse Population Liu, Zhi https://scholarship.miami.edu/discovery/delivery/01UOML_INST:ResearchRepository/12355224170002976?l#13355497430002976 Liu, Z. (2016). Identifying Genetic Risk Factors for Coronary Artery Angiographic Stenosis in a Genetically Diverse Population [University of Miami]. https://scholarship.miami.edu/discovery/fulldisplay/alma991031447280502976/01UOML_INST:ResearchR epository Embargo Downloaded On 2021/09/26 20:05:11 -0400 Please do not remove this page UNIVERSITY OF MIAMI IDENTIFYING GENETIC RISK FACTORS FOR CORONARY ARTERY ANGIOGRAPHIC STENOSIS IN A GENETICALLY DIVERSE POPULATION By Zhi Liu A DISSERTATION Submitted to the Faculty of the University of Miami in partial fulfillment of the requirements for the degree of Doctor of Philosophy Coral Gables, Florida August 2016 ©2016 Zhi Liu All Rights Reserved UNIVERSITY OF MIAMI A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy IDENTIFYING GENETIC RISK FACTORS FOR CORONARY ARTERY ANGIOGRAPHIC STENOSIS IN A GENETICALLY DIVERSE POPULATION Zhi Liu Approved: ________________ _________________ Gary W. Beecham, Ph.D. Liyong Wang, Ph.D. Assistant Professor of Human Associate Professor of Human Genetics Genetics ________________ _________________ Eden R. Martin, Ph.D. Guillermo Prado, Ph.D. Professor of Human Genetics Dean of the Graduate School ________________ Tatjana Rundek, M.D., Ph.D. Professor of Neurology LIU, ZHI (Ph.D., Human Genetics and Genomics) Identifying Genetic Risk Factors for Coronary Artery (August 2016) Angiographic Stenosis in a Genetically Diverse Population Abstract of a dissertation at the University of Miami. Dissertation supervised by Professor Gary W. -
A Comprehensive Protein–Protein Interactome for Yeast PAS Kinase 1 Reveals Direct Inhibition of Respiration Through the Phosphorylation of Cbf1
M BoC | ARTICLE A comprehensive protein–protein interactome for yeast PAS kinase 1 reveals direct inhibition of respiration through the phosphorylation of Cbf1 Desiree DeMillea, Benjamin T. Bikmanb, Andrew D. Mathisc, John T. Princec, Jordan T. Mackaya, Steven W. Sowaa, Tacie D. Halla, and Julianne H. Grosea aDepartment of Microbiology and Molecular Biology, bDepartment of Physiology and Developmental Biology, and cDepartment of Chemistry, Brigham Young University, Provo, UT 84602 ABSTRACT Per-Arnt-Sim (PAS) kinase is a sensory protein kinase required for glucose ho- Monitoring Editor meostasis in yeast, mice, and humans, yet little is known about the molecular mechanisms of Charles Boone its function. Using both yeast two-hybrid and copurification approaches, we identified the University of Toronto protein–protein interactome for yeast PAS kinase 1 (Psk1), revealing 93 novel putative pro- Received: Nov 1, 2013 tein binding partners. Several of the Psk1 binding partners expand the role of PAS kinase in Revised: Apr 28, 2014 glucose homeostasis, including new pathways involved in mitochondrial metabolism. In addi- Accepted: May 12, 2014 tion, the interactome suggests novel roles for PAS kinase in cell growth (gene/protein expres- sion, replication/cell division, and protein modification and degradation), vacuole function, and stress tolerance. In vitro kinase studies using a subset of 25 of these binding partners identified Mot3, Zds1, Utr1, and Cbf1 as substrates. Further evidence is provided for the in vivo phosphorylation of Cbf1 at T211/T212 and for the subsequent inhibition of respiration. This respiratory role of PAS kinase is consistent with the reported hypermetabolism of PAS kinase–deficient mice, identifying a possible molecular mechanism and solidifying the evolu- tionary importance of PAS kinase in the regulation of glucose homeostasis. -
Uncovering the Human Methyltransferasome*DS
Research © 2011 by The American Society for Biochemistry and Molecular Biology, Inc. This paper is available on line at http://www.mcponline.org Uncovering the Human Methyltransferasome*□S Tanya C. Petrossian and Steven G. Clarke‡ We present a comprehensive analysis of the human meth- core (2, 3, 5, 6, 15). The SPOUT methyltransferase superfamily yltransferasome. Primary sequences, predicted second- contains a distinctive knot structure and methylates RNA ary structures, and solved crystal structures of known substrates (16). SET domain methyltransferases catalyze the methyltransferases were analyzed by hidden Markov methylation of protein lysine residues with histones and ribo- models, Fisher-based statistical matrices, and fold recog- somal proteins as major targets (17–19). Smaller superfamilies nition prediction-based threading algorithms to create a with at least one three-dimensional structure available include model, or profile, of each methyltransferase superfamily. the precorrin-like methyltransferases (20), the radical SAM1 These profiles were used to scan the human proteome methyltransferases (21, 22), the MetH activation domain (23), database and detect novel methyltransferases. 208 pro- teins in the human genome are now identified as known or the Tyw3 protein involved in wybutosine synthesis (24), and putative methyltransferases, including 38 proteins that the homocysteine methyltransferases (25–27). Lastly, an inte- were not annotated previously. To date, 30% of these gral membrane methyltransferase family has been defined -
Downloaded from Ftp://Ftp.Uniprot.Org/ on July 3, 2019) Using Maxquant (V1.6.10.43) Search Algorithm
bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.385096; this version posted November 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. The proteomic landscape of resting and activated CD4+ T cells reveal insights into cell differentiation and function Yashwanth Subbannayya1, Markus Haug1, Sneha M. Pinto1, Varshasnata Mohanty2, Hany Zakaria Meås1, Trude Helen Flo1, T.S. Keshava Prasad2 and Richard K. Kandasamy1,* 1Centre of Molecular Inflammation Research (CEMIR), and Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology, N-7491 Trondheim, Norway 2Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India *Correspondence to: Professor Richard Kumaran Kandasamy Norwegian University of Science and Technology (NTNU) Centre of Molecular Inflammation Research (CEMIR) PO Box 8905 MTFS Trondheim 7491 Norway E-mail: [email protected] (Kandasamy R K) Tel.: +47-7282-4511 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.17.385096; this version posted November 17, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-ND 4.0 International license. Abstract CD4+ T cells (T helper cells) are cytokine-producing adaptive immune cells that activate or regulate the responses of various immune cells. -
Variable Selection Algorithms in Generalized Linear Models
VARIABLE SELECTION ALGORITHMS IN GENERALIZED LINEAR MODELS Juan Carlos Laria de la Cruz A DISSERTATION Submitted in partial fulfilment of the requirements for the degree of DOCTOR OF PHILOSOPHY (Mathematical Engineering) Universidad Carlos III de Madrid Advisors Rosa E. Lillo M. Carmen Aguilera-Morillo Tutor Rosa E. Lillo June, 2020 Variable selection algorithms in generalized linear models A DISSERTATION June, 2020 By Juan Carlos Laria de la Cruz Published by: UC3M, Department of Statistics, Av. Universidad 30, 28912 Leganés, Madrid Spain www.uc3m.es This work is licensed under Creative Commons Attribution – Non Commercial – Non Derivatives A mi madre Acknowledgements None of this work would have been possible without the continuous support, expert advice, motivation, constant dedication, and commit- ment of my thesis advisors and friends, Professors Rosa Lillo and Car- men Aguilera. I am deeply grateful to them. I would also like to thank my coauthors, and coworkers at the Depart- ment of Statistics. Many people have given me relevant suggestions and insights at different points during these years. Me being here has required so much patience and sacrifice by those involved in my education, that this work is theirs too. Not only my grandmother and my parents but also my school and university teach- ers authored this thesis. Special thanks to my family and my friends, who were always there for me, unconditionally, when I needed them. Contents published and presented The materials from the following sources are included in the thesis. Their inclusion is not indicated by typographical means or references, since they are fully embedded in each chapter indicated below. -
Characterizing Genomic Duplication in Autism Spectrum Disorder by Edward James Higginbotham a Thesis Submitted in Conformity
Characterizing Genomic Duplication in Autism Spectrum Disorder by Edward James Higginbotham A thesis submitted in conformity with the requirements for the degree of Master of Science Graduate Department of Molecular Genetics University of Toronto © Copyright by Edward James Higginbotham 2020 i Abstract Characterizing Genomic Duplication in Autism Spectrum Disorder Edward James Higginbotham Master of Science Graduate Department of Molecular Genetics University of Toronto 2020 Duplication, the gain of additional copies of genomic material relative to its ancestral diploid state is yet to achieve full appreciation for its role in human traits and disease. Challenges include accurately genotyping, annotating, and characterizing the properties of duplications, and resolving duplication mechanisms. Whole genome sequencing, in principle, should enable accurate detection of duplications in a single experiment. This thesis makes use of the technology to catalogue disease relevant duplications in the genomes of 2,739 individuals with Autism Spectrum Disorder (ASD) who enrolled in the Autism Speaks MSSNG Project. Fine-mapping the breakpoint junctions of 259 ASD-relevant duplications identified 34 (13.1%) variants with complex genomic structures as well as tandem (193/259, 74.5%) and NAHR- mediated (6/259, 2.3%) duplications. As whole genome sequencing-based studies expand in scale and reach, a continued focus on generating high-quality, standardized duplication data will be prerequisite to addressing their associated biological mechanisms. ii Acknowledgements I thank Dr. Stephen Scherer for his leadership par excellence, his generosity, and for giving me a chance. I am grateful for his investment and the opportunities afforded me, from which I have learned and benefited. I would next thank Drs. -
Functional Analysis of Rice Bidirectional Promoters
Michigan Technological University Digital Commons @ Michigan Tech Dissertations, Master's Theses and Master's Dissertations, Master's Theses and Master's Reports - Open Reports 2012 Functional analysis of rice bidirectional promoters Surendar R. Dhadi Michigan Technological University Follow this and additional works at: https://digitalcommons.mtu.edu/etds Part of the Biology Commons Copyright 2012 Surendar R. Dhadi Recommended Citation Dhadi, Surendar R., "Functional analysis of rice bidirectional promoters", Dissertation, Michigan Technological University, 2012. https://doi.org/10.37099/mtu.dc.etds/191 Follow this and additional works at: https://digitalcommons.mtu.edu/etds Part of the Biology Commons FUNCTIONAL ANALYSIS OF RICE BIDIRECTIONAL PROMOTERS By Surendar R Dhadi A DISSERTATION Submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY (Biological Sciences) MICHIGAN TECHNOLOGICAL UNIVERSITY 2012 Copyright © Surendar R Dhadi 2012 This dissertation, “Functional Analysis of Rice Bidirectional Promoters”, is hereby approved in partial fulfillment of the requirements for the Degree of DOCTOR OF PHILOSOPHY IN BIOLOGICAL SCIENCES. Department of Biological Sciences Signatures: Dissertation Advisor ________________________________________ Ramakrishna Wusirika Department Chair ________________________________________ K. Michael Gibson Date ________________________________________ TABLE OF CONTENTS List of Figures.......................................................................................................................... -
PTCD1 Is Required for Mitochondrial Oxidative-Phosphorylation: Possible Genetic Association with Alzheimer's Disease
This Accepted Manuscript has not been copyedited and formatted. The final version may differ from this version. A link to any extended data will be provided when the final version is posted online. Research Articles: Cellular/Molecular PTCD1 is required for mitochondrial oxidative-phosphorylation: possible genetic association with Alzheimer's disease Daniel Fleck1, Lilian Phu2, Erik Verschueren2, Trent Hinkle2, Mike Reichelt3, Tushar Bhangale4, Benjamin Haley5, Yuanyuan Wang1, Robert Graham4, Donald S. Kirkpatrick2, Morgan Sheng1 and Baris Bingol1 1Department of Neuroscience, Genentech Inc., South San Francisco, CA 94080, USA 2Department of Microchemistry, Proteomics and Lipidomics, Genentech Inc., South San Francisco, CA 94080, USA 3Department of Pathology, Genentech Inc., South San Francisco, CA 94080, USA 4Department of Human Genetics, Genentech Inc., South San Francisco, CA 94080, USA 5Department of Molecular Biology, Genentech Inc., South San Francisco, CA 94080, USA https://doi.org/10.1523/JNEUROSCI.0116-19.2019 Received: 14 January 2019 Revised: 26 March 2019 Accepted: 28 March 2019 Published: 4 April 2019 Author contributions: D.F., M.S., and B.B. designed research; D.F., L.P., and M.R. performed research; D.F., E.V., T.H., M.R., T.B., R.G., and D.S.K. analyzed data; D.F. wrote the first draft of the paper; D.F., L.P., E.V., T.H., M.R., T.B., B.H., Y.W., R.G., D.S.K., M.S., and B.B. edited the paper; D.F., M.S., and B.B. wrote the paper; B.H. and Y.W. contributed unpublished reagents/analytic tools. Conflict of Interest: The authors declare no competing financial interests.