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Beyond Gene Expression
Beyond gene expression Citation for published version (APA): Gupta, R. (2021). Beyond gene expression: novel methods and applications of transcript expression analyses in RNA-Seq. Maastricht University. https://doi.org/10.26481/dis.20210304rg Document status and date: Published: 01/01/2021 DOI: 10.26481/dis.20210304rg Document Version: Publisher's PDF, also known as Version of record Please check the document version of this publication: • A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal. -
Identification and Mechanistic Investigation of Recurrent Functional Genomic and Transcriptional Alterations in Advanced Prostat
Identification and Mechanistic Investigation of Recurrent Functional Genomic and Transcriptional Alterations in Advanced Prostate Cancer Thomas A. White A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2013 Reading Committee: Peter S. Nelson, Chair Janet L. Stanford Raymond J. Monnat Jay A. Shendure Program Authorized to Offer Degree: Molecular and Cellular Biology ©Copyright 2013 Thomas A. White University of Washington Abstract Identification and Mechanistic Investigation of Recurrent Functional Genomic and Transcriptional Alterations in Advanced Prostate Cancer Thomas A. White Chair of the Supervisory Committee: Peter S. Nelson, MD Novel functionally altered transcripts may be recurrent in prostate cancer (PCa) and may underlie lethal and advanced disease and the neuroendocrine small cell carcinoma (SCC) phenotype. We conducted an RNASeq survey of the LuCaP series of 24 PCa xenograft tumors from 19 men, and validated observations on metastatic tumors and PCa cell lines. Key findings include discovery and validation of 40 novel fusion transcripts including one recurrent chimera, many SCC-specific and castration resistance (CR) -specific novel splice isoforms, new observations on SCC-specific and TMPRSS2-ERG specific differential expression, the allele-specific expression of certain recurrent non- synonymous somatic single nucleotide variants (nsSNVs) previously discovered via exome sequencing of the same tumors, rgw ubiquitous A-to-I RNA editing of base excision repair (BER) gene NEIL1 as well as CDK13, a kinase involved in RNA splicing, and the SCC expression of a previously unannotated long noncoding RNA (lncRNA) at Chr6p22.2. Mechanistic investigation of the novel lncRNA indicates expression is regulated by derepression by master neuroendocrine regulator RE1-silencing transcription factor (REST), and may regulate some genes of axonogenesis and angiogenesis. -
MAFB Determines Human Macrophage Anti-Inflammatory
MAFB Determines Human Macrophage Anti-Inflammatory Polarization: Relevance for the Pathogenic Mechanisms Operating in Multicentric Carpotarsal Osteolysis This information is current as of September 25, 2021. Víctor D. Cuevas, Laura Anta, Rafael Samaniego, Emmanuel Orta-Zavalza, Juan Vladimir de la Rosa, Geneviève Baujat, Ángeles Domínguez-Soto, Paloma Sánchez-Mateos, María M. Escribese, Antonio Castrillo, Valérie Cormier-Daire, Miguel A. Vega and Ángel L. Corbí Downloaded from J Immunol published online 16 January 2017 http://www.jimmunol.org/content/early/2017/01/15/jimmun ol.1601667 http://www.jimmunol.org/ Supplementary http://www.jimmunol.org/content/suppl/2017/01/15/jimmunol.160166 Material 7.DCSupplemental Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision by guest on September 25, 2021 • No Triage! Every submission reviewed by practicing scientists • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2017 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. Published January 16, 2017, doi:10.4049/jimmunol.1601667 The Journal of Immunology MAFB Determines Human Macrophage Anti-Inflammatory Polarization: Relevance for the Pathogenic Mechanisms Operating in Multicentric Carpotarsal Osteolysis Vı´ctor D. -
US 2020/0078401 A1 VIJAYANAND Et Al
US 20200078401A1 IN ( 19 ) United States (12 ) Patent Application Publication ( 10) Pub . No .: US 2020/0078401 A1 VIJAYANAND et al. (43 ) Pub . Date : Mar. 12 , 2020 (54 ) COMPOSITIONS FOR CANCER (52 ) U.S. CI. TREATMENT AND METHODS AND USES CPC A61K 35/17 ( 2013.01) ; A61K 45/06 FOR CANCER TREATMENT AND ( 2013.01 ) ; C120 1/6886 ( 2013.01 ) ; A61P PROGNOSIS 35/00 (2018.01 ) ( 71 ) Applicants : La Jolla Institute for Allergy and Immunology , La Jolla , CA (US ) ; UNIVERSITY OF SOUTHAMPTON , (57 ) ABSTRACT Hampshire (GB ) (72 ) Inventors : Pandurangan VIJAYANAND , La Jolla , CA (US ) ; Christian Global transcriptional profiling of CTLs in tumors and OTTENSMEIER , Hampshire (GB ) ; adjacent non -tumor tissue from treatment- naive patients Anusha PreethiGANESAN , La Jolla , with early stage lung cancer revealed molecular features CA (US ) ; James CLARKE , Hampshire associated with robustness of anti - tumor immune responses . (GB ) ; Tilman SANCHEZ - ELSNER , Major differences in the transcriptional program of tumor Hampshire (GB ) infiltrating CTLswere observed that are shared across tumor subtypes . Pathway analysis revealed enrichment of genes in ( 21 ) Appl. No .: 16 / 465,983 cell cycle , T cell receptor ( TCR ) activation and co -stimula tion pathways , indicating tumor- driven expansion of pre ( 22 ) PCT Filed : Dec. 7 , 2017 sumed tumor antigen - specific CTLs. Marked heterogeneity in the expression ofmolecules associated with TCR activa ( 86 ) PCT No .: PCT /US2017 / 065197 tion and immune checkpoints such as 4-1BB , PD1, TIM3, $ 371 ( c ) ( 1 ) , was also observed and their expression was positively ( 2 ) Date : May 31 , 2019 correlated with the density of tumor- infiltrating CTLs. Tran scripts linked to tissue- resident memory cells ( TRM ), such Related U.S. -
Genetic Variants Underlying Cognitive Ability Gosso, M.F
VU Research Portal Common genetic variants underlying cognitive ability Gosso, M.F. 2008 document version Publisher's PDF, also known as Version of record Link to publication in VU Research Portal citation for published version (APA) Gosso, M. F. (2008). Common genetic variants underlying cognitive ability. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal ? Take down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. E-mail address: [email protected] Download date: 04. Oct. 2021 COMMON GENETIC VARIANTS UNDERLYING COGNITIVE ABILITY María Florencia Gosso Leescommissie: dr. W Crusio prof.dr. NG Martin dr. GJA Ramakers dr. S v/d Sluis prof.dr. CM van Duijn prof.dr. M Verhage This thesis was supported by the Universitair Stimulerings Fonds (grant number 96/22), the Human Frontiers of Science Program (grant number rg0154/1998-B), the Netherlands Organization for Scientific Research (NWO) grants 904-57-94 and NWO/SPI 56-464-14192, and by the Centre for Medical Systems Biology (CMSB), a center of excellence approved by the Netherlands Genomics Initiative/Netherlands Organization for Scientific Research (NWO). -
Identifying Recurrent Patterns of Chromatin Modifications at Regulatory Regions on Genome
Identifying Recurrent Patterns of Chromatin Modifications at Regulatory Regions on Genome DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Nan Meng Graduate Program in Computer Science and Engineering The Ohio State University 2015 Dissertation Committee: Dr. Raghu Machiraju, Adviser Dr. Kun Huang, Co-adviser Dr. Yuejie Chi Copyright by Nan Meng 2015 Abstract Epigenetics is an important regulation layer of DNA transcription in cells. Post- translational modification is one of the most studied aspects of epigenetics. The distribution of chromatin modifications at known regulatory regions could provide invaluable information on epigenetic regulations of DNA transcription. Firstly, a pipeline was developed to quantitatively identify and analyze distinct recurrent distribution patterns of single chromatin modification at regulatory regions. The clustering based method identified several recurrent patterns in cell lines from different tissue types. One particular pattern identified at promoter regions indicates activation of gene transcription. Further investigation show genes displaying this pattern carry important roles in cell development and differentiation. Later the study was extended to regulatory regions for long non-coding RNAs. This study shows that similar epigenetic regulatory functions regulate lncRNAs as well. Then a computational framework was developed to study combinatorial patterns of multiple chromatin modifications. Results show that recurrent combinatorial patterns provide more insights on subtle details of epigenetic regulation. However, it is computationally challenging and unnecessary to include all chromatin modifications as some of their distributions may be correlated. Our framework provides an efficient way to select a subset of chromatin modifications that best represents the recurrent combinatorial patterns. -
Genome-Wide Association Studies of Autoimmune Vitiligo Identify 23 New Risk Loci and Highlight Key Pathways and Regulatory Variants
CORE Metadata, citation and similar papers at core.ac.uk Provided by University of Liverpool RepositoryHHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Nat Genet Manuscript Author . Author manuscript; Manuscript Author available in PMC 2017 April 10. Published in final edited form as: Nat Genet. 2016 November ; 48(11): 1418–1424. doi:10.1038/ng.3680. Genome-wide association studies of autoimmune vitiligo identify 23 new risk loci and highlight key pathways and regulatory variants Ying Jin1,2, Genevieve Andersen1, Daniel Yorgov3, Tracey M Ferrara1, Songtao Ben1, Kelly M Brownson1, Paulene J Holland1, Stanca A Birlea1,4, Janet Siebert5, Anke Hartmann6, Anne Lienert6, Nanja van Geel7, Jo Lambert7, Rosalie M Luiten8, Albert Wolkerstorfer8, JP Wietze van der Veen8,9, Dorothy C Bennett10, Alain Taïeb11, Khaled Ezzedine11, E Helen Kemp12, David J Gawkrodger12, Anthony P Weetman12, Sulev Kõks13, Ele Prans13, Külli Kingo14, Maire Karelson14, Margaret R Wallace15, Wayne T McCormack16, Andreas Overbeck17, Silvia Moretti18, Roberta Colucci18, Mauro Picardo19, Nanette B Silverberg20,21, Mats Olsson22, Yan Valle23, Igor Korobko23,24, Markus Böhm25, Henry W. Lim26, Iltefat Hamzavi26, Li Zhou26, Qing-Sheng Mi26, Pamela R. Fain1,2, Stephanie A Santorico1,3,27, and Richard A Spritz1,2 1Human Medical Genetics and Genomics Program, University of Colorado School of Medicine, Aurora, Colorado, USA 2Department of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado, USA 3Department of Mathematical and Statistical -
(Ppp1r14) Family of Protein Phosphatase 1 Inhibitors in Teleosts
International Journal of Molecular Sciences Article The Evolution of Duplicated Genes of the Cpi-17/Phi-1 (ppp1r14) Family of Protein Phosphatase 1 Inhibitors in Teleosts Irene Lang 1, Guneet Virk 1, Dale C. Zheng 1, Jason Young 1, Michael J. Nguyen 1, Rojin Amiri 1, Michelle Fong 1, Alisa Arata 1, Katia S. Chadaideh 1,2, Susan Walsh 3 and Douglas C. Weiser 1,* 1 Department of Biological Sciences, University of the Pacific, Stockton, CA 98211, USA; [email protected]fic.edu (I.L.); [email protected]fic.edu (G.V.); dzheng@pacific.edu (D.C.Z.); [email protected]fic.edu (J.Y.); [email protected]fic.edu (M.J.N.); [email protected]fic.edu (R.A.); [email protected]fic.edu (M.F.); [email protected]fic.edu (A.A.); [email protected] (K.S.C.) 2 Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA 3 Life Sciences, Soka University of America, Aliso Viejo, CA 92656, USA; [email protected] * Correspondence: dweiser@pacific.edu; Tel.: +1-209-946-2955 Received: 29 July 2020; Accepted: 7 August 2020; Published: 9 August 2020 Abstract: The Cpi-17 (ppp1r14) gene family is an evolutionarily conserved, vertebrate specific group of protein phosphatase 1 (PP1) inhibitors. When phosphorylated, Cpi-17 is a potent inhibitor of myosin phosphatase (MP), a holoenzyme complex of the regulatory subunit Mypt1 and the catalytic subunit PP1. Myosin phosphatase dephosphorylates the regulatory myosin light chain (Mlc2) and promotes actomyosin relaxation, which in turn, regulates numerous cellular processes including smooth muscle contraction, cytokinesis, cell motility, and tumor cell invasion. We analyzed zebrafish homologs of the Cpi-17 family, to better understand the mechanisms of myosin phosphatase regulation. -
A Compendium of Physical Exercise-Related Human Genes: an ’Omic Scale Analysis
OriginalA compendium Paper of physical exercise-related human genes DOI: 10.5114/biolsport.2018.70746 Biol. Sport 2018;35:3-11 A compendium of physical exercise-related human genes: an ’omic scale analysis 1 1 AUTHORS: Christina Pacheco , Stela Mirla da Silva Felipe , Milca Magalhães Dias de Carvalho Corresponding author: Soares1, Juliana Osório Alves1, Paula Matias Soares1, José Henrique Leal-Cardoso1, Adriano Vânia Marilande Ceccatto César Carneiro Loureiro1, Alex Soares Marreiros Ferraz2, Denise Pires de Carvalho3, Vânia R. Dr. Silas Munguba, 1700 Instituto Superior de Ciências 1 Marilande Ceccatto Biomédicas, Universidade Estadual do Ceará, Fortaleza, 1 Instituto Superior de Ciências Biomédicas, Universidade Estadual do Ceará, Fortaleza, CE, Brazil CE, Brazil. E-mail: [email protected] 2 Instituto de Educação Física e Esportes, Universidade Federal do Ceará, Fortaleza, CE, Brazil 3 Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, RJ, Brazil ABSTRACT: Regular exercise is an exogenous factor of gene regulation with numerous health benefits. The study aimed to evaluate human genes linked to physical exercise in an ‘omic scale, addressing biological questions to the generated database. Three literature databases were searched with the terms ‘exercise’, ‘fitness’, ‘physical activity’, ‘genetics’ and ‘gene expression’. For additional references, papers were scrutinized and a text- mining tool was used. Papers linking genes to exercise in humans through microarray, RNA-Seq, RT-PCR and genotyping studies were included. Genes were extracted from the collected literature, together with information on exercise protocol, experimental design, gender, age, number of individuals, analytical method, fold change and statistical data. The ‘omic scale dataset was characterized and evaluated with bioinformatics tools searching for gene expression patterns, functional meaning and gene clusters. -
The Extracellular Bone Marrow Microenvironment – a Proteomic Comparison of Constitutive Protein Release by in Vitro Cultured Osteoblasts and Mesenchymal Stem Cells
SUPPLEMENTARY INFORMATION The extracellular bone marrow microenvironment – a proteomic comparison of constitutive protein release by in vitro cultured osteoblasts and mesenchymal stem cells Elise Aasebø 1, Even Birkeland 2, Frode Selheim 2, Frode Berven 2, Annette K. Brenner 1 and Øystein Bruserud 1, 3,* 1 Department of Clinical Science, University of Bergen, Bergen, Norway; [email protected], [email protected], [email protected] 2 The Proteomics Facility of the University of Bergen (PROBE), University of Bergen, Bergen, Norway; [email protected], [email protected], [email protected] 3 Department of Medicine, Haukeland University Hospital, Bergen, Norway; [email protected] 1 Table S1. Proteins released by in vitro cultured MSCs and/or osteoblasts; a summary showing important groups of proteins. Only structural groups/main groups including at least five members are shown. EXTRACELLULAR MATRIX (n=34) Collagens (n=22) COL1A1 Collagen alpha-1(I) chain COL1A2 Collagen alpha-2(I) chain COL2A1 Collagen alpha-1(II) chain;Collagen alpha-1(II) chain;Chondrocalcin COL3A1 Collagen alpha-1(III) chain COL4A1 Collagen alpha-1(IV) chain;Arresten COL4A2 Collagen alpha-2(IV) chain;Canstatin COL5A1 Collagen alpha-1(V) chain COL5A2 Collagen alpha-2(V) chain COL5A3 Collagen alpha-3(V) chain COL6A1 Collagen alpha-1(VI) chain COL6A2 Collagen alpha-2(VI) chain COL6A2 Collagen alpha-2(VI) chain COL6A3 Collagen alpha-3(VI) chain COL7A1 Collagen alpha-1(VII) chain COL8A1 Collagen alpha-1(VIII) chain;Vastatin COL10A1 Collagen