Estimation of Non-Null SNP Effect Size Distributions Enables the Detection
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Bayesian Hierarchical Modeling of High-Throughput Genomic Data with Applications to Cancer Bioinformatics and Stem Cell Differentiation
BAYESIAN HIERARCHICAL MODELING OF HIGH-THROUGHPUT GENOMIC DATA WITH APPLICATIONS TO CANCER BIOINFORMATICS AND STEM CELL DIFFERENTIATION by Keegan D. Korthauer A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Statistics) at the UNIVERSITY OF WISCONSIN–MADISON 2015 Date of final oral examination: 05/04/15 The dissertation is approved by the following members of the Final Oral Committee: Christina Kendziorski, Professor, Biostatistics and Medical Informatics Michael A. Newton, Professor, Statistics Sunduz Kele¸s,Professor, Biostatistics and Medical Informatics Sijian Wang, Associate Professor, Biostatistics and Medical Informatics Michael N. Gould, Professor, Oncology © Copyright by Keegan D. Korthauer 2015 All Rights Reserved i in memory of my grandparents Ma and Pa FL Grandma and John ii ACKNOWLEDGMENTS First and foremost, I am deeply grateful to my thesis advisor Christina Kendziorski for her invaluable advice, enthusiastic support, and unending patience throughout my time at UW-Madison. She has provided sound wisdom on everything from methodological principles to the intricacies of academic research. I especially appreciate that she has always encouraged me to eke out my own path and I attribute a great deal of credit to her for the successes I have achieved thus far. I also owe special thanks to my committee member Professor Michael Newton, who guided me through one of my first collaborative research experiences and has continued to provide key advice on my thesis research. I am also indebted to the other members of my thesis committee, Professor Sunduz Kele¸s,Professor Sijian Wang, and Professor Michael Gould, whose valuable comments, questions, and suggestions have greatly improved this dissertation. -
Proquest Dissertations
nm u Ottawa L'Universite canadienne Canada's university run FACULTE DES ETUDES SUPERIEURES ^=1 FACULTY OF GRADUATE AND ET POSTOCTORALES U Ottawa POSDOCTORAL STUDIES L'Univeisittf canathenne Canada's university Anna Francina Jackson „_„^^.^^_^^^.„^ M.Sc. (Cellular and Molecular Medicine) __„.___._ Department of Cellular and Molecular Medicine The Functional Characterization of Wdr68 Regulation of Pax7 Activity in Myogenesis TITRE DE LA THESE / TITLE OF THESIS M. Rudnicki „„„„_.___ N;LWij3CT:Berg©ron RJjcreaton_ Gary W. Slater Le Doyen de la Faculte des etudes superieures et postdoctorales / Dean of the Faculty of Graduate and Postdoctoral Studies The Functional Characterization of Wdr68 Regulation of Pax7 Activity in Myogenesis Anna Francina Jackson This thesis is submitted to the Faculty of Graduate and Postdoctoral Studies in partial fulfillment of the requirements for a Master of Science degree in Cellular and Molecular Medicine. Department of Cellular and Molecular Medicine Faculty of Medicine University of Ottawa May 14, 2010 ©Anna Francina Jackson, Ottawa, Canada, 2010 Library and Archives Bibliotheque et 1*1 Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington OttawaONK1A0N4 OttawaONK1A0N4 Canada Canada Your file Votre reference ISBN: 978-0-494-74221-1 Our file Notre reference ISBN: 978-0-494-74221-1 NOTICE: AVIS: The author has granted a non L'auteur a accorde une licence non exclusive exclusive license allowing Library and permettant a la Bibliotheque -
New Resources for Transcription Analysis and Genome Fugu
Downloaded from genome.cshlp.org on July 6, 2011 - Published by Cold Spring Harbor Laboratory Press Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation Melody S. Clark, Yvonne J.K. Edwards, Dan Peterson, et al. Genome Res. 2003 13: 2747-2753 Access the most recent version at doi:10.1101/gr.1691503 References This article cites 51 articles, 26 of which can be accessed free at: http://genome.cshlp.org/content/13/12/2747.full.html#ref-list-1 Article cited in: http://genome.cshlp.org/content/13/12/2747.full.html#related-urls 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 To subscribe to Genome Research go to: http://genome.cshlp.org/subscriptions Cold Spring Harbor Laboratory Press Downloaded from genome.cshlp.org on July 6, 2011 - Published by Cold Spring Harbor Laboratory Press Resource Fugu ESTs: New Resources for Transcription Analysis and Genome Annotation Melody S. Clark,1,7,8 Yvonne J.K. Edwards,1 Dan Peterson,2 Sandra W. Clifton,2 Amanda J. Thompson,1 Masahide Sasaki,3 Yutaka Suzuki,3 Kiyoshi Kikuchi,5,6 Shugo Watabe,5 Koichi Kawakami,4 Sumio Sugano,3 Greg Elgar,1 and Stephen L. Johnson2 1MRC Rosalind Franklin Centre for Genomics Research, (formerly known as the MRC UK HGMP Resource Centre), Genome Campus, Hinxton, Cambridge, CB10 1SB, UK; 2Department of Genetics, Washington University Medical School, St Louis, Missouri 63110, USA; 3The Institute of Medical Science, The University of Tokyo, Shirokanedai, -
Identification of TMEM131L As a Novel Regulator of Thymocyte Proliferation in Humans
Identification of TMEM131L as a Novel Regulator of Thymocyte Proliferation in Humans This information is current as Nesrine Maharzi, Véronique Parietti, Elisabeth Nelson, of September 25, 2021. Simona Denti, Macarena Robledo-Sarmiento, Niclas Setterblad, Aude Parcelier, Marika Pla, François Sigaux, Jean Claude Gluckman and Bruno Canque J Immunol 2013; 190:6187-6197; Prepublished online 20 May 2013; Downloaded from doi: 10.4049/jimmunol.1300400 http://www.jimmunol.org/content/190/12/6187 Supplementary http://www.jimmunol.org/content/suppl/2013/05/21/jimmunol.130040 http://www.jimmunol.org/ Material 0.DC1 References This article cites 44 articles, 20 of which you can access for free at: http://www.jimmunol.org/content/190/12/6187.full#ref-list-1 Why The JI? Submit online. by guest on September 25, 2021 • Rapid Reviews! 30 days* from submission to initial decision • 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 © 2013 by The American Association of Immunologists, -
Multidrug Transporter MRP4/ABCC4 As a Key Determinant of Pancreatic
www.nature.com/scientificreports OPEN Multidrug transporter MRP4/ ABCC4 as a key determinant of pancreatic cancer aggressiveness A. Sahores1, A. Carozzo1, M. May1, N. Gómez1, N. Di Siervi1, M. De Sousa Serro1, A. Yanef1, A. Rodríguez‑González2, M. Abba3, C. Shayo2 & C. Davio1* Recent fndings show that MRP4 is critical for pancreatic ductal adenocarcinoma (PDAC) cell proliferation. Nevertheless, the signifcance of MRP4 protein levels and function in PDAC progression is still unclear. The aim of this study was to determine the role of MRP4 in PDAC tumor aggressiveness. Bioinformatic studies revealed that PDAC samples show higher MRP4 transcript levels compared to normal adjacent pancreatic tissue and circulating tumor cells express higher levels of MRP4 than primary tumors. Also, high levels of MRP4 are typical of high-grade PDAC cell lines and associate with an epithelial-mesenchymal phenotype. Moreover, PDAC patients with high levels of MRP4 depict dysregulation of pathways associated with migration, chemotaxis and cell adhesion. Silencing MRP4 in PANC1 cells reduced tumorigenicity and tumor growth and impaired cell migration. Transcriptomic analysis revealed that MRP4 silencing alters PANC1 gene expression, mainly dysregulating pathways related to cell-to-cell interactions and focal adhesion. Contrarily, MRP4 overexpression signifcantly increased BxPC-3 growth rate, produced a switch in the expression of EMT markers, and enhanced experimental metastatic incidence. Altogether, our results indicate that MRP4 is associated with a more aggressive phenotype in PDAC, boosting pancreatic tumorigenesis and metastatic capacity, which could fnally determine a fast tumor progression in PDAC patients. Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal human malignancies, due to its late diag- nosis, inherent resistance to treatment and early dissemination 1. -
DYRK1A Binds to an Evolutionarily Conserved WD40-Repeat Title Protein WDR68 and Induces Its Nuclear Translocation
DYRK1A binds to an evolutionarily conserved WD40-repeat Title protein WDR68 and induces its nuclear translocation. Author(s) Miyata, Yoshihiko; Nishida, Eisuke Citation Biochimica et biophysica acta (2011), 1813(10): 1728-1739 Issue Date 2011-10 URL http://hdl.handle.net/2433/148020 © 2011 Elsevier B.V.; This is not the published version. Please cite only the published version.; この論文は出版社版であり Right ません。引用の際には出版社版をご確認ご利用ください 。 Type Journal Article Textversion author Kyoto University *REVISED Manuscript (text UNmarked) Click here to view linked References DYRK1A binds to an evolutionarily conserved WD40-repeat protein WDR68 and induces its nuclear translocation Yoshihiko Miyata*, Eisuke Nishida Department of Cell and Developmental Biology, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Kyoto 606-8502, Japan * Corresponding author. Department of Cell & Developmental Biology, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan. Tel.: +81-75-753-4231; fax: +81-75-753-4235. 1 ABSTRACT DYRK1A is encoded in the Down’s syndrome critical region on human chromosome 21, and plays an important role in the functional and developmental regulation of many types of cells, including neuronal cells. Here we have identified WDR68, an evolutionarily conserved protein with WD40-repeat domains, as a cellular binding partner of DYRK1A. WDR68 was originally identified in petunia as AN11 that controls the pigmentation of flowers by stimulating the transcription of anthocyanin biosynthetic genes. Experiments with RNA interference showed that WDR68 was indispensable for the optimal proliferation and survival of mammalian cultured cell, and WDR68 depletion induced cell apoptosis. DYRK1A and DYRK1B, but not DYRK2, DYRK3, or DYRK4, bound to endogenous and expressed WDR68. -
WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization I International Bureau (10) International Publication Number (43) International Publication Date WO 2019/079361 Al 25 April 2019 (25.04.2019) W 1P O PCT (51) International Patent Classification: CA, CH, CL, CN, CO, CR, CU, CZ, DE, DJ, DK, DM, DO, C12Q 1/68 (2018.01) A61P 31/18 (2006.01) DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, C12Q 1/70 (2006.01) HR, HU, ID, IL, IN, IR, IS, JO, JP, KE, KG, KH, KN, KP, KR, KW, KZ, LA, LC, LK, LR, LS, LU, LY, MA, MD, ME, (21) International Application Number: MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, PCT/US2018/056167 OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, RW, SA, (22) International Filing Date: SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, 16 October 2018 (16. 10.2018) TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (25) Filing Language: English (84) Designated States (unless otherwise indicated, for every kind of regional protection available): ARIPO (BW, GH, (26) Publication Language: English GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, ST, SZ, TZ, (30) Priority Data: UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ, 62/573,025 16 October 2017 (16. 10.2017) US TM), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK, EE, ES, FI, FR, GB, GR, HR, HU, ΓΕ , IS, IT, LT, LU, LV, (71) Applicant: MASSACHUSETTS INSTITUTE OF MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM, TECHNOLOGY [US/US]; 77 Massachusetts Avenue, TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW, Cambridge, Massachusetts 02139 (US). -
The Landscape of Human Mutually Exclusive Splicing
bioRxiv preprint doi: https://doi.org/10.1101/133215; this version posted May 2, 2017. 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 landscape of human mutually exclusive splicing Klas Hatje1,2,#,*, Ramon O. Vidal2,*, Raza-Ur Rahman2, Dominic Simm1,3, Björn Hammesfahr1,$, Orr Shomroni2, Stefan Bonn2§ & Martin Kollmar1§ 1 Group of Systems Biology of Motor Proteins, Department of NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany 2 Group of Computational Systems Biology, German Center for Neurodegenerative Diseases, Göttingen, Germany 3 Theoretical Computer Science and Algorithmic Methods, Institute of Computer Science, Georg-August-University Göttingen, Germany § Corresponding authors # Current address: Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Basel, Switzerland $ Current address: Research and Development - Data Management (RD-DM), KWS SAAT SE, Einbeck, Germany * These authors contributed equally E-mail addresses: KH: [email protected], RV: [email protected], RR: [email protected], DS: [email protected], BH: [email protected], OS: [email protected], SB: [email protected], MK: [email protected] - 1 - bioRxiv preprint doi: https://doi.org/10.1101/133215; this version posted May 2, 2017. 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. -
Open Thesis FINAL3.Pdf
THE PENNSYLVANIA STATE UNIVERSITY SCHREYER HONORS COLLEGE DEPARTMENT OF BIOLOGY THE IDENTIFICATION AND CHARACTERIZATION OF SUFU INTERACTING PROTEINS EMILY VALERIO SPRING 2013 A thesis submitted in partial fulfillment of the requirements for a baccalaureate degree in Biology with honors in Biology Reviewed and approved* by the following: Aimin Liu Associate Professor of Biology Thesis Supervisor Gong Chen Associate Professor of Biology Honors Adviser * Signatures are on file in the Schreyer Honors College. i ABSTRACT The Hedgehog (Hh) pathway, activated by a special family of proteins, is a prominent pathway in mammalian development and also in the formation of various cancers. When interacting with cells, Hh ligands are responsible for enhancing target Hh gene expression through the activation of Gli-transcriptional activators. Suppressor of Fused (Sufu) is a specific Gli-interacting protein that functions in negatively regulating Gli activity and by doing so, suppressing Gli-activated tumor formation. The extent of how Sufu functions is not yet understood in mammals. In an effort to identify proteins that may interact with Sufu in this pathway, over 50 candidate proteins were identified through a yeast-two hybrid screen. Through much background research, four particular proteins were selected due to their known function and location in the cell: ran-binding protein 9 (RanBP9), transmembrane 131-like precursor (T131L), COP9 signalosome complex subunit 1 isoform (Gps1), and hypothetical protein LOC67513. After performing co-immunoprecipitation assays, we confirmed interactions with T131L, Gps1 and LOC67513. These proteins have also been recognized to interact with both structural domains of Sufu, the N-terminal domain and C-terminal domain. -
Nº Ref Uniprot Proteína Péptidos Identificados Por MS/MS 1 P01024
Document downloaded from http://www.elsevier.es, day 26/09/2021. This copy is for personal use. Any transmission of this document by any media or format is strictly prohibited. Nº Ref Uniprot Proteína Péptidos identificados 1 P01024 CO3_HUMAN Complement C3 OS=Homo sapiens GN=C3 PE=1 SV=2 por 162MS/MS 2 P02751 FINC_HUMAN Fibronectin OS=Homo sapiens GN=FN1 PE=1 SV=4 131 3 P01023 A2MG_HUMAN Alpha-2-macroglobulin OS=Homo sapiens GN=A2M PE=1 SV=3 128 4 P0C0L4 CO4A_HUMAN Complement C4-A OS=Homo sapiens GN=C4A PE=1 SV=1 95 5 P04275 VWF_HUMAN von Willebrand factor OS=Homo sapiens GN=VWF PE=1 SV=4 81 6 P02675 FIBB_HUMAN Fibrinogen beta chain OS=Homo sapiens GN=FGB PE=1 SV=2 78 7 P01031 CO5_HUMAN Complement C5 OS=Homo sapiens GN=C5 PE=1 SV=4 66 8 P02768 ALBU_HUMAN Serum albumin OS=Homo sapiens GN=ALB PE=1 SV=2 66 9 P00450 CERU_HUMAN Ceruloplasmin OS=Homo sapiens GN=CP PE=1 SV=1 64 10 P02671 FIBA_HUMAN Fibrinogen alpha chain OS=Homo sapiens GN=FGA PE=1 SV=2 58 11 P08603 CFAH_HUMAN Complement factor H OS=Homo sapiens GN=CFH PE=1 SV=4 56 12 P02787 TRFE_HUMAN Serotransferrin OS=Homo sapiens GN=TF PE=1 SV=3 54 13 P00747 PLMN_HUMAN Plasminogen OS=Homo sapiens GN=PLG PE=1 SV=2 48 14 P02679 FIBG_HUMAN Fibrinogen gamma chain OS=Homo sapiens GN=FGG PE=1 SV=3 47 15 P01871 IGHM_HUMAN Ig mu chain C region OS=Homo sapiens GN=IGHM PE=1 SV=3 41 16 P04003 C4BPA_HUMAN C4b-binding protein alpha chain OS=Homo sapiens GN=C4BPA PE=1 SV=2 37 17 Q9Y6R7 FCGBP_HUMAN IgGFc-binding protein OS=Homo sapiens GN=FCGBP PE=1 SV=3 30 18 O43866 CD5L_HUMAN CD5 antigen-like OS=Homo -
Noncoding Rnas As Novel Pancreatic Cancer Targets
NONCODING RNAS AS NOVEL PANCREATIC CANCER TARGETS by Amy Makler A Thesis Submitted to the Faculty of The Charles E. Schmidt College of Science In Partial Fulfillment of the Requirements for the Degree of Master of Science Florida Atlantic University Boca Raton, FL August 2018 Copyright 2018 by Amy Makler ii ACKNOWLEDGEMENTS I would first like to thank Dr. Narayanan for his continuous support, constant encouragement, and his gentle, but sometimes critical, guidance throughout the past two years of my master’s education. His faith in my abilities and his belief in my future success ensured I continue down this path of research. Working in Dr. Narayanan’s lab has truly been an unforgettable experience as well as a critical step in my future endeavors. I would also like to extend my gratitude to my committee members, Dr. Binninger and Dr. Jia, for their support and suggestions regarding my thesis. Their recommendations added a fresh perspective that enriched our initial hypothesis. They have been indispensable as members of my committee, and I thank them for their contributions. My parents have been integral to my successes in life and their support throughout my education has been crucial. They taught me to push through difficulties and encouraged me to pursue my interests. Thank you, mom and dad! I would like to thank my boyfriend, Joshua Disatham, for his assistance in ensuring my writing maintained a logical progression and flow as well as his unwavering support. He was my rock when the stress grew unbearable and his encouraging words kept me pushing along. -
Mammalian PRC1 Complexes: Compositional Complexity and Diverse Molecular Mechanisms
International Journal of Molecular Sciences Review Mammalian PRC1 Complexes: Compositional Complexity and Diverse Molecular Mechanisms Zhuangzhuang Geng 1 and Zhonghua Gao 1,2,3,* 1 Departments of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA; [email protected] 2 Penn State Hershey Cancer Institute, Hershey, PA 17033, USA 3 The Stem Cell and Regenerative Biology Program, Penn State College of Medicine, Hershey, PA 17033, USA * Correspondence: [email protected] Received: 6 October 2020; Accepted: 5 November 2020; Published: 14 November 2020 Abstract: Polycomb group (PcG) proteins function as vital epigenetic regulators in various biological processes, including pluripotency, development, and carcinogenesis. PcG proteins form multicomponent complexes, and two major types of protein complexes have been identified in mammals to date, Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2). The PRC1 complexes are composed in a hierarchical manner in which the catalytic core, RING1A/B, exclusively interacts with one of six Polycomb group RING finger (PCGF) proteins. This association with specific PCGF proteins allows for PRC1 to be subdivided into six distinct groups, each with their own unique modes of action arising from the distinct set of associated proteins. Historically, PRC1 was considered to be a transcription repressor that deposited monoubiquitylation of histone H2A at lysine 119 (H2AK119ub1) and compacted local chromatin. More recently, there is increasing evidence that demonstrates the transcription activation role of PRC1. Moreover, studies on the higher-order chromatin structure have revealed a new function for PRC1 in mediating long-range interactions. This provides a different perspective regarding both the transcription activation and repression characteristics of PRC1.