DOCSLIB.ORG

Supple Tables 181003-2

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supple Tables 181003-2 Supplementary file 2: Gene expression changes in the brain mononuclear cells of CD47 KO mice This table contains a list of all gene expression changes in the brain mononuclear cells of CD47 KO mice ( > 2-fold: Log2 ratio > 1 or < -1) Expression of total 16,544 genes was detected in both or either of the genotypes. Genes (with different probe set ID#) found in both of the increased and decreased gene groups were excluded from the table. 1,323 and 2,286 genes were markedly (> 2-fold) increased and decreased, respectively, in CD47 KO compared with WT mice. column name description probe set ID# Affymetrix probe set ID number for Mouse 430 2.0 Genome Arrays gene gene description symbol gene symbol accession NCBI accession number Log2 ratio Gene expression fold change expressed as Log2 (KO/WT) probe set ID# gene symbol accession Log2 ratio 1423527_at coiled coil glutamate rich protein 1 Ccer1 AK006212 7.05 1445945_at expressed sequence AU021880 AU021880 BG068075 6.88 1457245_at disrupted in renal carcinoma 2 (human) Dirc2 AW988060 6.49 1429495_at transmembrane protein 107 Tmem107 AV007348 6.40 1458849_at N-acylsphingosine amidohydrolase 2 Asah2 BB234186 6.07 1425994_a_at N-acylsphingosine amidohydrolase 2 Asah2 AB037111 1.45 Rpl31 /// Rpl31- 1436144_at ribosomal protein L31 /// ribosomal protein L31, pseudogene 1 2 BG802091 5.94 ps12 1444594_at T-box 3 Tbx3 AA024086 5.88 1441354_at expressed sequence AU018740 AU018740 BG069312 5.79 1434425_at trichohyalin Tchh AI597080 5.66 1427447_a_at TRIO and F-actin binding protein Triobp BC003984 5.56 1447139_at B cell CLL/lymphoma 7C Bcl7c BM234097 5.20 1446516_at B cell CLL/lymphoma 7C Bcl7c BB176719 2.22 1423476_at solute carrier family 46, member 2 Slc46a2 BB329435 5.19 1441845_at calcyphosphine 2 Caps2 BB388044 5.15 1454442_at BCL2/adenovirus E1B interacting protein 2 Bnip2 AK017785 5.12 1440158_x_at coiled-coil-helix-coiled-coil-helix domain containing 7 Chchd7 BB209663 5.09 1437092_at CAP-GLY domain containing linker protein family, member 4 Clip4 AV042829 5.04 1458014_at AF4/FMR2 family, member 2 Aff2 BB245809 5.02 TAF9B RNA polymerase II, TATA box binding protein (TBP)-associated 1447829_x_at Taf9b BB431174 5.00 factor 1435471_at zinc finger protein 708 Zfp708 BE994129 4.98 1454213_at armadillo repeat containing 9 Armc9 AK019512 4.93 1428399_a_at armadillo repeat containing 9 Armc9 AK017564 2.11 1417207_at dishevelled 2, dsh homolog (Drosophila) Dvl2 BF466091 4.90 1454160_at glutamate receptor interacting protein 1, opposite strand 1 Grip1os1 AK019561 4.90 1446974_at phosphoinositide kinase, FYVE finger containing Pikfyve BM220925 4.85 1447444_at UBX domain protein 11 Ubxn11 AW495835 4.71 1457323_at single-pass membrane protein with coiled-coil domains 3 Smco3 AI846508 4.65 1424630_a_at breast cancer 1 Brca1 U31625 4.54 1451417_at breast cancer 1 Brca1 U31625 4.33 1439981_at thymocyte expressed, positive selection associated 1 Tespa1 BB198298 4.51 1438747_at RIKEN cDNA A930006K02 gene A930006K02Rik BF020563 4.44 1442196_at RIKEN cDNA A930006K02 gene A930006K02Rik BB174109 1.19 1444686_at family with sequence similarity 173, member B Fam173b BB279561 4.40 1435572_at RIKEN cDNA 2310014L17 gene 2310014L17Rik AV232798 4.40 1442292_at Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6 Arhgef6 BB474042 4.35 1425102_a_at angiotensin I converting enzyme (peptidyl-dipeptidase A) 2 Ace2 AB053181 4.33 1447368_at maestro heat-like repeat family member 2A Mroh2a BF019000 4.21 1453458_at RIKEN cDNA 9430019C24 gene 9430019C24Rik BM121183 4.19 1441118_at family with sequence similarity 222, member B Fam222b BB389461 4.13 1419220_at xin actin-binding repeat containing 1 Xirp1 NM_011724 4.07 a disintegrin-like and metallopeptidase (reprolysin type) with 1444253_at Adamts18 BM117857 4.06 thrombospondin type 1 motif, 18 a disintegrin-like and metallopeptidase (reprolysin type) with 1446247_at Adamts18 BB125422 2.87 thrombospondin type 1 motif, 18 1460030_at HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 Hecw1 BB355811 4.05 1440656_at HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1 Hecw1 BB458541 1.06 1425985_s_at mannan-binding lectin serine peptidase 1 Masp1 AB049755 4.05 1419677_at mannan-binding lectin serine peptidase 1 Masp1 NM_008555 1.10 1453584_at serine/threonine kinase 36 Stk36 AK007188 4.04 1456777_at maltase-glucoamylase Mgam BB072761 4.03 1416693_at forkhead box C2 Foxc2 NM_013519 3.97 probe set ID# gene symbol accession Log2 ratio 1442579_at RIKEN cDNA 9330111N05 gene 9330111N05Rik BB306259 3.94 1433361_at RIKEN cDNA 4930527F18 gene 4930527F18Rik AK015915 3.94 Gm3417 /// predicted gene 3417 /// predicted gene 3448 /// t-complex-associated 1421682_a_at Gm3448 /// NM_011560 3.92 testis expressed 3 Tcte3 1440888_at oxytocin receptor Oxtr BB551848 3.88 1455980_a_at growth arrest-specific 2 like 3 Gas2l3 BB770972 3.87 1437244_at growth arrest-specific 2 like 3 Gas2l3 BB770972 1.73 1433652_at immunoglobulin superfamily, member 1 Igsf1 AV245981 3.78 1438589_at immunoglobulin superfamily, member 1 Igsf1 BB023061 2.43 Mus musculus adult male testis cDNA, RIKEN full-length enriched library, AK076909 /// 1459129_at clone:4930548A09 product:unclassifiable, full insert sequence. /// --- /// Gm20616 /// AV270194 3.78 predicted gene 20616 Gm20616 1444197_at Ras and Rab interactor-like Rinl BB163345 3.77 A630072M18Ri 1427081_at RIKEN cDNA A630072M18 gene BB246700 3.76 k 1455382_at ZW10 interactor Zwint AV130073 3.76 1456862_at sine oculis-related homeobox 4 Six4 AI893638 3.75 1415935_at SPARC related modular calcium binding 2 Smoc2 NM_022315 3.74 1430484_at RIKEN cDNA 8430428J23 gene 8430428J23Rik AK018447 3.72 1422922_at RecQ protein-like 4 Recql4 NM_058214 3.72 1420735_at gamma-aminobutyric acid (GABA) C receptor, subunit rho 2 Gabrr2 AF024621 3.70 1432275_at inhibitor of kappaB kinase beta Ikbkb AK011359 3.69 1454184_a_at inhibitor of kappaB kinase beta Ikbkb AK011359 1.55 1430895_at RIKEN cDNA 2010109A12 gene 2010109A12Rik BF018972 3.67 1441950_s_at RIKEN cDNA 2010109A12 gene 2010109A12Rik AV064063 3.57 1441951_x_at RIKEN cDNA 2010109A12 gene 2010109A12Rik AV064063 2.74 1459544_at lipoyltransferase 1 Lipt1 BB180990 3.65 1417281_a_at matrix metallopeptidase 23 Mmp23 NM_011985 3.61 1430589_at phosphatidylinositol glycan anchor biosynthesis, class H Pigh AK020902 3.61 1450215_at recoverin Rcvrn NM_009038 3.57 1449502_at deleted in azoospermia-like Dazl NM_010021 3.54 1446425_at EF-hand calcium binding domain 14 Efcab14 BB075807 3.54 1459211_at GLI-Kruppel family member GLI2 Gli2 AW546128 3.53 1457626_at DNA segment, Chr 3, Wayne State University 106, expressed D3Wsu106e AA407555 3.49 1429932_at RIKEN cDNA 4930566F21 gene 4930566F21Rik AV215452 3.49 1430879_at RIKEN cDNA C030008P14 gene C030008P14Rik BB283753 3.47 1442079_at sphingomyelin synthase 1 Sgms1 BM238389 3.47 1450190_at zinc finger protein 106 Zfp106 NM_009165 3.46 1439279_at RIKEN cDNA 3110007F17 gene 3110007F17Rik AV339304 3.42 1430312_at tryptophan rich basic protein Wrb AK021091 3.41 Gm20515 /// 1440714_at predicted gene 20515 /// --- BB083283 3.40 Gm20515 1439712_at integrator complex subunit 10 Ints10 BB668046 3.40 1450094_at RAN binding protein 17 Ranbp17 NM_023146 3.39 1427238_at F-box protein 15 Fbxo15 AF176530 3.35 1422396_s_at achaete-scute complex homolog 2 (Drosophila) Ascl2 NM_008554 3.33 1456714_at WW domain containing E3 ubiquitin protein ligase 2 Wwp2 BB217820 3.32 1428800_a_at pseudouridylate synthase 7 homolog (S. cerevisiae)-like Pus7l AK019372 3.32 Gm13235 /// predicted gene 13235 /// predicted gene 13242 /// predicted gene 13247 Gm13242 /// 1445924_at BG065840 3.30 /// predicted gene, 21082 Gm13247 /// Gm21082 1419519_at insulin-like growth factor 1 Igf1 NM_010512 3.29 1452014_a_at insulin-like growth factor 1 Igf1 AF440694 1.97 1420471_at hypocretin Hcrt NM_010410 3.29 1445445_s_at prostaglandin E receptor 1 (subtype EP1) Ptger1 BB283614 3.27 1445653_at cDNA sequence BC031361 BC031361 BB825492 3.27 1431547_at RIKEN cDNA 4930435F18 gene 4930435F18Rik AK015323 3.25 1449153_at matrix metallopeptidase 12 Mmp12 BC019135 3.20 1419141_at crystallin, gamma D Crygd NM_007776 3.19 1444744_at death inducer-obliterator 1 Dido1 BF461970 3.19 1448719_at transcriptional adaptor 3 Tada3 AK003405 3.19 1458246_at uncharacterized LOC102632313 LOC102632313 BM934733 3.17 1457824_at phospholipid scramblase 1 Plscr1 AI504076 3.15 1440000_at RIKEN cDNA E330013P04 gene E330013P04Rik BG069958 3.14 1419751_x_at solute carrier family 22, member 27 Slc22a27 NM_134256 3.14 1457582_at ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome Uty BB528233 3.14 probe set ID# gene symbol accession Log2 ratio 1426598_at ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome Uty BB742957 1.76 1422247_a_at ubiquitously transcribed tetratricopeptide repeat gene, Y chromosome Uty NM_009484 1.05 1427227_at gamma-aminobutyric acid (GABA) A receptor, subunit gamma 1 Gabrg1 AF156490 3.13 1427026_at myosin, heavy polypeptide 4, skeletal muscle Myh4 AJ278733 3.11 1444771_at ankyrin repeat and BTB (POZ) domain containing 2 Abtb2 BB228490 3.11 1444386_at phosphodiesterase 1C Pde1c BB388392 3.10 1422330_at glucagon-like peptide 1 receptor Glp1r NM_021332 3.05 1444163_at NIMA (never in mitosis gene a)-related expressed kinase 5 Nek5 BB049667 3.04 1448426_at sarcosine dehydrogenase Sardh BI217574 3.04 Gm19569 /// 1456990_at predicted gene, 19569 /// --- BB199484 3.02 RP24-364K9.3 1460103_at predicted gene, 26598 Gm26598 BG071165 3.01 1457273_at teneurin transmembrane protein 2 Tenm2 BM899576 3.01 1429990_at
Load more

Recommended publications
  • The Switch from Fermentation to Respiration in Saccharomyces Cerevisiae Is Regulated by the Ert1 Transcriptional Activator/Repressor
    INVESTIGATION The Switch from Fermentation to Respiration in Saccharomyces cerevisiae Is Regulated by the Ert1 Transcriptional Activator/Repressor Najla Gasmi,* Pierre-Etienne Jacques,† Natalia Klimova,† Xiao Guo,§ Alessandra Ricciardi,§ François Robert,†,** and Bernard Turcotte*,‡,§,1 ‡Department of Medicine, *Department of Biochemistry, and §Department of Microbiology and Immunology, McGill University Health Centre, McGill University, Montreal, QC, Canada H3A 1A1, †Institut de recherches cliniques de Montréal, Montréal, QC, Canada H2W 1R7, and **Département de Médecine, Faculté de Médecine, Université de Montréal, QC, Canada H3C 3J7 ABSTRACT In the yeast Saccharomyces cerevisiae, fermentation is the major pathway for energy production, even under aerobic conditions. However, when glucose becomes scarce, ethanol produced during fermentation is used as a carbon source, requiring a shift to respiration. This adaptation results in massive reprogramming of gene expression. Increased expression of genes for gluconeogenesis and the glyoxylate cycle is observed upon a shift to ethanol and, conversely, expression of some fermentation genes is reduced. The zinc cluster proteins Cat8, Sip4, and Rds2, as well as Adr1, have been shown to mediate this reprogramming of gene expression. In this study, we have characterized the gene YBR239C encoding a putative zinc cluster protein and it was named ERT1 (ethanol regulated transcription factor 1). ChIP-chip analysis showed that Ert1 binds to a limited number of targets in the presence of glucose. The strongest enrichment was observed at the promoter of PCK1 encoding an important gluconeogenic enzyme. With ethanol as the carbon source, enrichment was observed with many additional genes involved in gluconeogenesis and mitochondrial function. Use of lacZ reporters and quantitative RT-PCR analyses demonstrated that Ert1 regulates expression of its target genes in a manner that is highly redundant with other regulators of gluconeogenesis.
    [Show full text]
  • A Genetically Modified Dermal Micro-Organ Expressing Erythropoietin
    (19) & (11) EP 2 377 401 A1 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 19.10.2011 Bulletin 2011/42 A01N 63/00 (2006.01) A01N 65/00 (2009.01) C12N 5/00 (2006.01) C12N 5/02 (2006.01) (2010.01) (21) Application number: 11174205.2 C12N 5/071 (22) Date of filing: 29.04.2004 (84) Designated Contracting States: • Bukhman, Mordechay AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 21891 Carmiel (IL) HU IE IT LI LU MC NL PL PT RO SE SI SK TR • Stern, Baruch, S. Designated Extension States: 34366 Haifa (IL) AL HR LT LV MK • Shalhevet, David 36090 Kiryat Tivon (IL) (30) Priority: 01.05.2003 US 466793 P • Shavitt, Menachem, D. 06.08.2003 US 492754 P 20142 D.N. Misgav (IL) • Pearlman, Andrew, L. (62) Document number(s) of the earlier application(s) in 20164 D.N. Miscav (IL) accordance with Art. 76 EPC: • Noam, Shani 04760621.5 / 1 653 807 30900 Zichron Yaakov (IL) • Almon, Einat (71) Applicant: Medgenics, Inc. 23840 Timrat (IL) Palo Alto, CA 94303 (US) (74) Representative: Modiano, Micaela Nadia (72) Inventors: Modiano & Partners • Bellomo, Stephen, F. Thierschstrasse 11 30900 Zichron Yaakov (IL) 80538 München (DE) • Lippin, Itzhak 42920 Moshav Beit Yitzhak (IL) Remarks: • Piva, Guillermo, Alberto This application was filed on 15-07-2011 as a Winston Salem, NC North Carolina 27104 (US) divisional application to the application mentioned • Rosenberg, Lior under INID code 62. 84965 Omer (IL) (54) A genetically modified dermal micro-organ expressing erythropoietin (57) The present invention is directed to a genetically cro-organ
    [Show full text]
  • A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
    Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated.
    [Show full text]
  • Identification of Potential Proteases for Abdominal Aortic Aneurysm by Weighted Gene Coexpression Network Analysis
    Genome Identification of potential proteases for abdominal aortic aneurysm by weighted gene coexpression network analysis Journal: Genome Manuscript ID gen-2020-0041.R1 Manuscript Type: Article Date Submitted by the 28-Jun-2020 Author: Complete List of Authors: Zhang, Hui; Peking Union Medical College Hospital, Department of Vascular Surgery Yang, Dan; Chinese Academy of Medical Sciences and Peking Union Medical College, Department of Computational Biology and Bioinformatics,Draft Institute of Medicinal Plant Development Chen, Siliang; Peking Union Medical College Hospital, Department of Vascular Surgery Li, Fangda; Peking Union Medical College Hospital, Department of Vascular Surgery Cui, Liqiang; Peking Union Medical College Hospital, Department of Vascular Surgery Liu, Zhili; Peking Union Medical College Hospital, Department of Vascular Surgery Shao, Jiang; Peking Union Medical College Hospital, Department of Vascular Surgery Chen, Yuexin; Peking Union Medical College Hospital, Department of Vascular Surgery Liu, Bao; Peking Union Medical College Hospital, Department of Vascular Surgery Zheng, Yuehong; Peking Union Medical College Hospital, Department of Vascular Surgery Abdominal aortic aneurysm, next-generation sequencing, WGCNA, Keyword: proteases, matrix metalloproteinase Is the invited manuscript for consideration in a Special Not applicable (regular submission) Issue? : https://mc06.manuscriptcentral.com/genome-pubs Page 1 of 35 Genome 1 Identification of potential proteases for abdominal aortic aneurysm by weighted gene 2 coexpression network analysis 3 Short title: WGCNA identifies crucial proteases in AAA 4 5 Hui Zhang1, Dan Yang2, Siliang Chen1, Fangda Li1, Liqiang Cui1, Zhili Liu1, Jiang Shao1, Yuexin 6 Chen1, Bao Liu1, Yuehong Zheng1. 7 1Department of Vascular Surgery, Peking Union Medical College Hospital, Beijing 100730, PR 8 China; 2Department of Computational Biology and Bioinformatics, Institute of Medicinal Plant 9 Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 10 100730, PR China.
    [Show full text]
  • Transcriptomic Analysis of Native Versus Cultured Human and Mouse Dorsal Root Ganglia Focused on Pharmacological Targets Short
    bioRxiv preprint doi: https://doi.org/10.1101/766865; this version posted September 12, 2019. 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. Transcriptomic analysis of native versus cultured human and mouse dorsal root ganglia focused on pharmacological targets Short title: Comparative transcriptomics of acutely dissected versus cultured DRGs Andi Wangzhou1, Lisa A. McIlvried2, Candler Paige1, Paulino Barragan-Iglesias1, Carolyn A. Guzman1, Gregory Dussor1, Pradipta R. Ray1,#, Robert W. Gereau IV2, # and Theodore J. Price1, # 1The University of Texas at Dallas, School of Behavioral and Brain Sciences and Center for Advanced Pain Studies, 800 W Campbell Rd. Richardson, TX, 75080, USA 2Washington University Pain Center and Department of Anesthesiology, Washington University School of Medicine # corresponding authors [email protected], [email protected] and [email protected] Funding: NIH grants T32DA007261 (LM); NS065926 and NS102161 (TJP); NS106953 and NS042595 (RWG). The authors declare no conflicts of interest Author Contributions Conceived of the Project: PRR, RWG IV and TJP Performed Experiments: AW, LAM, CP, PB-I Supervised Experiments: GD, RWG IV, TJP Analyzed Data: AW, LAM, CP, CAG, PRR Supervised Bioinformatics Analysis: PRR Drew Figures: AW, PRR Wrote and Edited Manuscript: AW, LAM, CP, GD, PRR, RWG IV, TJP All authors approved the final version of the manuscript. 1 bioRxiv preprint doi: https://doi.org/10.1101/766865; this version posted September 12, 2019. 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.
    [Show full text]
  • Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases
    International Journal of Molecular Sciences Review Effects of Glycosylation on the Enzymatic Activity and Mechanisms of Proteases Peter Goettig Structural Biology Group, Faculty of Molecular Biology, University of Salzburg, Billrothstrasse 11, 5020 Salzburg, Austria; [email protected]; Tel.: +43-662-8044-7283; Fax: +43-662-8044-7209 Academic Editor: Cheorl-Ho Kim Received: 30 July 2016; Accepted: 10 November 2016; Published: 25 November 2016 Abstract: Posttranslational modifications are an important feature of most proteases in higher organisms, such as the conversion of inactive zymogens into active proteases. To date, little information is available on the role of glycosylation and functional implications for secreted proteases. Besides a stabilizing effect and protection against proteolysis, several proteases show a significant influence of glycosylation on the catalytic activity. Glycans can alter the substrate recognition, the specificity and binding affinity, as well as the turnover rates. However, there is currently no known general pattern, since glycosylation can have both stimulating and inhibiting effects on activity. Thus, a comparative analysis of individual cases with sufficient enzyme kinetic and structural data is a first approach to describe mechanistic principles that govern the effects of glycosylation on the function of proteases. The understanding of glycan functions becomes highly significant in proteomic and glycomic studies, which demonstrated that cancer-associated proteases, such as kallikrein-related peptidase 3, exhibit strongly altered glycosylation patterns in pathological cases. Such findings can contribute to a variety of future biomedical applications. Keywords: secreted protease; sequon; N-glycosylation; O-glycosylation; core glycan; enzyme kinetics; substrate recognition; flexible loops; Michaelis constant; turnover number 1.
    [Show full text]
  • Genes in Eyecare Geneseyedoc 3 W.M
    Genes in Eyecare geneseyedoc 3 W.M. Lyle and T.D. Williams 15 Mar 04 This information has been gathered from several sources; however, the principal source is V. A. McKusick’s Mendelian Inheritance in Man on CD-ROM. Baltimore, Johns Hopkins University Press, 1998. Other sources include McKusick’s, Mendelian Inheritance in Man. Catalogs of Human Genes and Genetic Disorders. Baltimore. Johns Hopkins University Press 1998 (12th edition). http://www.ncbi.nlm.nih.gov/Omim See also S.P.Daiger, L.S. Sullivan, and B.J.F. Rossiter Ret Net http://www.sph.uth.tmc.edu/Retnet disease.htm/. Also E.I. Traboulsi’s, Genetic Diseases of the Eye, New York, Oxford University Press, 1998. And Genetics in Primary Eyecare and Clinical Medicine by M.R. Seashore and R.S.Wappner, Appleton and Lange 1996. M. Ridley’s book Genome published in 2000 by Perennial provides additional information. Ridley estimates that we have 60,000 to 80,000 genes. See also R.M. Henig’s book The Monk in the Garden: The Lost and Found Genius of Gregor Mendel, published by Houghton Mifflin in 2001 which tells about the Father of Genetics. The 3rd edition of F. H. Roy’s book Ocular Syndromes and Systemic Diseases published by Lippincott Williams & Wilkins in 2002 facilitates differential diagnosis. Additional information is provided in D. Pavan-Langston’s Manual of Ocular Diagnosis and Therapy (5th edition) published by Lippincott Williams & Wilkins in 2002. M.A. Foote wrote Basic Human Genetics for Medical Writers in the AMWA Journal 2002;17:7-17. A compilation such as this might suggest that one gene = one disease.
    [Show full text]
  • Supp. Table S2: Domains and Protein Families with a Putative Role in Host-Symbiont Interactions
    Supp. Table S2: Domains and protein families with a putative role in host-symbiont interactions. The domains and protein families listed here were included in the comparisons in Figure 5 and Supp. Figure S5, which show the percentage of the respective protein groups in the Riftia symbiont metagenome and in metagenomes of other symbiotic and free-living organisms. % bacterial, total number bacterial: Percentage and total number of bacterial species in which this domain is found in the SMART database (January 2019). Domain name Pfam/SMART % bacterial (total Literature/comment annotation number bacterial) Alpha-2- alpha-2- A2M: 42.05% (2057) A2Ms: protease inhibitors which are important for eukaryotic macroglobulin macroglobulin innate immunity, if present in prokaryotes apparently fulfill a family (A2M), similar role, e.g. protection against host proteases (1) including N- terminal MG1 domain ANAPC Anaphase- APC2: 0 Ubiquitin ligase, important for cell cycle control in eukaryotes (2) promoting complex Bacterial proteins might interact with ubiquitination pathways in subunits the host (3) Ankyrin Ankyrin repeats 10.88% (8348) Mediate protein-protein interactions without sequence specificity (4) Sponge symbiont ankyrin-repeat proteins inhibit amoebal phagocytosis (5) Present in sponge microbiome metatranscriptomes, putative role in symbiont-host interactions (6) Present in obligate intracellular amoeba symbiont Candidatus Amoebophilus asiaticus genome, probable function in interactions with the host (7) Armadillo Armadillo repeats 0.83% (67)
    [Show full text]
  • University of California, San Diego
    UNIVERSITY OF CALIFORNIA, SAN DIEGO A Lipidomic Perspective on Inflammatory Macrophage Eicosanoid Signaling A Thesis submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Chemistry by Paul Christopher Norris Committee in charge: Professor Edward A. Dennis, Chair Professor Pieter C. Dorrestein Professor Partho Ghosh Professor Christopher K. Glass Professor Michael J. Sailor 2013 The Dissertation of Paul Christopher Norris is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Chair University of California, San Diego 2013 iii DEDICATION To my parents, Darrell and Kathy, for always allowing me to think (and choose) for myself. iv TABLE OF CONTENTS Signature page ............................................................................................................................ iii Dedication .................................................................................................................................. iv Table of contents ......................................................................................................................... v List of symbols and abbreviations ........................................................................................... viii List of figures ............................................................................................................................. xi List of tables ............................................................................................................................
    [Show full text]
  • Human Gene Copy Number Spectra Analysis in Congenital Heart Malformations Aoy Tomita-Mitchell Medical College of Wisconsin
    CORE Metadata, citation and similar papers at core.ac.uk Provided by epublications@Marquette Marquette University e-Publications@Marquette Mathematics, Statistics and Computer Science Mathematics, Statistics and Computer Science, Faculty Research and Publications Department of 5-1-2012 Human gene copy number spectra analysis in congenital heart malformations Aoy Tomita-Mitchell Medical College of Wisconsin Donna K. Mahnke Medical College of Wisconsin Craig Struble Marquette University, [email protected] Maureen E. Tuffnell Marquette University Karl D. Stamm Marquette University See next page for additional authors Accepted version. Physiological Genomics, Vol. 44, No. 9 (May 2012): 518-541. DOI. © 2012 The American Physiological Society. Used with permission. Authors Aoy Tomita-Mitchell, Donna K. Mahnke, Craig Struble, Maureen E. Tuffnell, Karl D. Stamm, Mats Hidestrand, Susan Harris, Mary A. Goetsch, Pippa Simpson, David P. Bick, Ulrich Broeckel, Andrew N. Pelech, James S. Tweddell, and Michael Mitchell This article is available at e-Publications@Marquette: https://epublications.marquette.edu/mscs_fac/272 NOT THE PUBLISHED VERSION; this is the author’s final, peer-reviewed manuscript. The published version may be accessed by following the link in the citation at the bottom of the page. Human Gene Copy Number Spectra Analysis in Congenital Heart Malformations Aoy Tomita-Mitchell Department of Surgery, Division of Cardiothoracic Surgery; Biotechnology and Bioengineering Center; Human and Molecular Genetics Center; Medical College of Wisconsin; Milwaukee, WI Donna K. Mahnke Department of Surgery, Division of Cardiothoracic Surgery; Biotechnology and Bioengineering Center; Human and Molecular Genetics Center; Medical College of Wisconsin; Milwaukee, WI Craig A. Struble Department of Mathematics, Statistics and Computer Science; Marquette University; Milwaukee, WI Maureen E.
    [Show full text]
  • Differential Gene Expression in Oligodendrocyte Progenitor Cells, Oligodendrocytes and Type II Astrocytes
    Tohoku J. Exp. Med., 2011,Differential 223, 161-176 Gene Expression in OPCs, Oligodendrocytes and Type II Astrocytes 161 Differential Gene Expression in Oligodendrocyte Progenitor Cells, Oligodendrocytes and Type II Astrocytes Jian-Guo Hu,1,2,* Yan-Xia Wang,3,* Jian-Sheng Zhou,2 Chang-Jie Chen,4 Feng-Chao Wang,1 Xing-Wu Li1 and He-Zuo Lü1,2 1Department of Clinical Laboratory Science, The First Affiliated Hospital of Bengbu Medical College, Bengbu, P.R. China 2Anhui Key Laboratory of Tissue Transplantation, Bengbu Medical College, Bengbu, P.R. China 3Department of Neurobiology, Shanghai Jiaotong University School of Medicine, Shanghai, P.R. China 4Department of Laboratory Medicine, Bengbu Medical College, Bengbu, P.R. China Oligodendrocyte precursor cells (OPCs) are bipotential progenitor cells that can differentiate into myelin-forming oligodendrocytes or functionally undetermined type II astrocytes. Transplantation of OPCs is an attractive therapy for demyelinating diseases. However, due to their bipotential differentiation potential, the majority of OPCs differentiate into astrocytes at transplanted sites. It is therefore important to understand the molecular mechanisms that regulate the transition from OPCs to oligodendrocytes or astrocytes. In this study, we isolated OPCs from the spinal cords of rat embryos (16 days old) and induced them to differentiate into oligodendrocytes or type II astrocytes in the absence or presence of 10% fetal bovine serum, respectively. RNAs were extracted from each cell population and hybridized to GeneChip with 28,700 rat genes. Using the criterion of fold change > 4 in the expression level, we identified 83 genes that were up-regulated and 89 genes that were down-regulated in oligodendrocytes, and 92 genes that were up-regulated and 86 that were down-regulated in type II astrocytes compared with OPCs.
    [Show full text]
  • 140503 IPF Signatures Supplement Withfigs Thorax
    Supplementary material for Heterogeneous gene expression signatures correspond to distinct lung pathologies and biomarkers of disease severity in idiopathic pulmonary fibrosis Daryle J. DePianto1*, Sanjay Chandriani1⌘*, Alexander R. Abbas1, Guiquan Jia1, Elsa N. N’Diaye1, Patrick Caplazi1, Steven E. Kauder1, Sabyasachi Biswas1, Satyajit K. Karnik1#, Connie Ha1, Zora Modrusan1, Michael A. Matthay2, Jasleen Kukreja3, Harold R. Collard2, Jackson G. Egen1, Paul J. Wolters2§, and Joseph R. Arron1§ 1Genentech Research and Early Development, South San Francisco, CA 2Department of Medicine, University of California, San Francisco, CA 3Department of Surgery, University of California, San Francisco, CA ⌘Current address: Novartis Institutes for Biomedical Research, Emeryville, CA. #Current address: Gilead Sciences, Foster City, CA. *DJD and SC contributed equally to this manuscript §PJW and JRA co-directed this project Address correspondence to Paul J. Wolters, MD University of California, San Francisco Department of Medicine Box 0111 San Francisco, CA 94143-0111 [email protected] or Joseph R. Arron, MD, PhD Genentech, Inc. MS 231C 1 DNA Way South San Francisco, CA 94080 [email protected] 1 METHODS Human lung tissue samples Tissues were obtained at UCSF from clinical samples from IPF patients at the time of biopsy or lung transplantation. All patients were seen at UCSF and the diagnosis of IPF was established through multidisciplinary review of clinical, radiological, and pathological data according to criteria established by the consensus classification of the American Thoracic Society (ATS) and European Respiratory Society (ERS), Japanese Respiratory Society (JRS), and the Latin American Thoracic Association (ALAT) (ref. 5 in main text). Non-diseased normal lung tissues were procured from lungs not used by the Northern California Transplant Donor Network.
    [Show full text]