DOCSLIB.ORG

Genbank Accession No. Gene Symbol Expression Ratio (Shm2/Shc9) Title

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Genbank Accession No. Gene Symbol Expression Ratio (Shm2/Shc9) Title Expression GenBank Pathway Gene symbol ratio Title Accession No. (KEGG pathway No.) (shM2/shC9) Transcribed locus, moderately similar to XP_522534.1 similar to BM991882.1 -- 41.03783209 Interferon-induced transmembrane protein 3 (Interferon-inducible -- protein 1-8U) [Pan troglodytes] NM_006435.1 IFITM2 36.18790782 Interferon induced transmembrane protein 2 (1-8D) -- BG567659.1 -- 26.87432934 Transcribed locus -- NM_021034.1 IFITM3 21.4012685 Interferon induced transmembrane protein 3 (1-8U) -- NM_006398.2 UBD 19.77554843 Ubiquitin D -- NM_021175.2 HAMP 14.56061138 Hepcidin antimicrobial peptide -- Cytokine-cytokine receptor interaction(hsa04060);;Toll-like NM_001565.1 CXCL10 12.67290311 Chemokine (C-X-C motif) ligand 10 receptor signaling pathway(hsa04620) NM_002658.1 PLAU 10.33977708 plasminogen activator, urokinase (PLAU) Complement and coagulation cascades(hsa04610) Cytokine-cytokine receptor interaction(hsa04060);;Toll-like NM_000584.2 IL8 9.82456723 Interleukin 8 receptor signaling pathway(hsa04620) NM_002260.2 KLRC3 7.92786087 Killer cell lectin-like receptor subfamily C, member 2 -- Tissue inhibitor of metalloproteinase 1 (erythroid potentiating NM_003254.1 TIMP1 7.728329543 -- activity, collagenase inhibitor) NM_002083.2 GPX2 7.48286105 Glutathione peroxidase 2 (gastrointestinal) Glutathione metabolism(hsa00480) NM_000064.1 C3 6.734646525 Complement component 3 Complement and coagulation cascades(hsa04610) NM_001387.2 DPYSL3 6.471008184 Dihydropyrimidinase-like 3 -- NM_024501.1 HOXD1 6.402739992 Homeo box D1 -- NM_181428.1 BCAS4 6.03386637 thymosin-like 6 (TMSL6) -- Secreted phosphoprotein 1 (osteopontin, bone sialoprotein I, early NM_000582.2 SPP1 5.84964084 -- T-lymphocyte activation 1) NM_024053.2 C22orf18 5.703370995 chromosome 22 open reading frame 18 (C22orf18) -- NM_001826.1 CKS1B 5.665161366 CDC28 protein kinase regulatory subunit 1B -- BQ025821.1 ECHDC3 5.541731238 Enoyl Coenzyme A hydratase domain containing 3 -- NM_004750.2 CRLF1 5.499982302 Cytokine receptor-like factor 1 -- NM_002089.1 CXCL2 5.343372695 Chemokine (C-X-C motif) ligand 2 Cytokine-cytokine receptor interaction(hsa04060) BM550825.1 BCAS3 5.180394077 Breast carcinoma amplified sequence 3 -- NM_005567.2 LGALS3BP 5.155349597 Lectin, galactoside-binding, soluble, 3 binding protein -- NM_032348.2 MGC3047 5.095 Limitrin -- NM_005213.2 CSTA 4.848435323 Cystatin A (stefin A) -- NM_000700.1 ANXA1 4.808650551 Annexin A1 -- BX647607.1 -- 4.801172039 CDNA FLJ35776 fis, clone TESTI2005326 -- NM_173636.3 C19orf14 4.743421975 Chromosome 19 open reading frame 14 -- NM_024743.2 FLJ21934 4.685219418 Hypothetical protein FLJ21934 -- NM_001853.2 COL9A3 4.610418583 Collagen, type IX, alpha 3 -- NM_001826.1 CKS1B 4.590975416 CDC28 protein kinase regulatory subunit 1B -- H49355.1 C18orf17 4.5279631 Chromosome 18 open reading frame 17 -- NM_000480.1 AMPD3 4.465449503 Adenosine monophosphate deaminase (isoform E) Purine metabolism(hsa00230) Galactose metabolism(hsa00052);;Pentose and glucuronate interconversions(hsa00040);;Glycerolipid NM_001628.2 AKR1B1 4.378794367 Aldo-keto reductase family 1, member B1 (aldose reductase) metabolism(hsa00561);;Fructose and mannose metabolism(hsa00051);;Pyruvate metabolism(hsa00620) NM_001233.3 CAV2 4.354894801 Caveolin 2 Focal adhesion(hsa04510) NM_017723.1 FLJ20245 4.304083947 Hypothetical protein FLJ20245 -- Transcribed locus, moderately similar to NP_872301.1 hypothetical AV741130.1 -- 4.297652391 -- protein FLJ25224 [Homo sapiens] AK098460.1 -- 4.204725666 CDNA FLJ25594 fis, clone JTH13012 -- AI022672.1 GYPA 4.204610538 Glycophorin A (includes MN blood group) -- NM_000186.1 CFH 4.175217364 Complement factor H Complement and coagulation cascades(hsa04610) NM_006156.1 NEDD8 4.055517751 Neural precursor cell expressed, developmentally down-regulated -- NM_030940.2 HBLD2 3.98978063 HESB like domain containing 2 (HBLD2) -- Homocysteine-inducible, endoplasmic reticulum stress-inducible, NM_014685.1 HERPUD1 3.98054902 -- ubiquitin-like domain member 1 BI561641.1 LOC339903 3.969699826 Hypothetical protein LOC339903 -- Galactose metabolism(hsa00052);;Pentose and glucuronate interconversions(hsa00040);;Glycerolipid NM_001628.2 AKR1B1 3.950058562 Aldo-keto reductase family 1, member B1 (aldose reductase) metabolism(hsa00561);;Fructose and mannose metabolism(hsa00051);;Pyruvate metabolism(hsa00620) BG208475.1 -- 3.898607463 RST27977 Athersys RAGE Library Homo sapiens cDNA -- NM_030576.2 MGC10986 3.877993952 Hypothetical protein MGC10986 -- NM_000033.2 ABCD1 3.840836383 ATP-binding cassette, sub-family D (ALD), member 1 -- NM_003256.2 TIMP4 3.837855971 Tissue inhibitor of metalloproteinase 4 -- NM_017971.2 MRPL20 3.828562089 Mitochondrial ribosomal protein L20 -- ATPase, Cu++ transporting, alpha polypeptide (Menkes NM_000052.1 ATP7A 3.811283455 -- syndrome) (ATP7A) AK025577.1 FLJ21924 3.75817066 Hypothetical protein FLJ21924 -- Myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, BX649158.1 MLLT4 3.750336172 Adherens junction(hsa04520);;Tight junction(hsa04530) Drosophila); translocated to, 4 NM_002901.1 RCN1 3.745237157 Reticulocalbin 1, EF-hand calcium binding domain -- Transcribed locus, weakly similar to NP_872601.1 ubiquitously BU177664.1 -- 3.743398919 -- transcribed tetratricopeptide repeat gene, Y-linked [Homo NM_002084.2 GPX3 3.73772019 Glutathione peroxidase 3 (plasma) Glutathione metabolism(hsa00480) AA075723.1 -- 3.700235223 Transcribed locus -- NM_021200.1 PLEKHB1 3.696267337 Pleckstrin homology domain containing, family B (evectins) -- NM_002402.2 MEST 3.688530281 Mesoderm specific transcript homolog (mouse) -- NM_052972.2 LRG1 3.685575934 Leucine-rich alpha-2-glycoprotein 1 -- Arginine and proline metabolism(hsa00330);;Nicotinate and NM_018399.2 VNN3 3.662951519 Vanin 3 nicotinamide metabolism(hsa00760);;Pantothenate and CoA biosynthesis(hsa00770) inhibitor of kappa light polypeptide gene enhancer in B-cells, MAPK signaling pathway(hsa04010);;Toll-like receptor signaling NM_014002.1 IKBKE 3.651060782 kinase epsilon (IKBKE), mRNA pathway(hsa04620) BX648336.1 ZNF451 3.649707138 KIAA1702 protein -- NM_025079.1 FLJ23231 3.647622359 Hypothetical protein FLJ23231 -- NM_004467.3 FGL1 3.624243972 Fibrinogen-like 1 -- BC006173.1 C14orf151 3.586836633 Chromosome 14 open reading frame 151 -- CB321977.1 -- 3.584914842 Transcribed locus -- T63636 yc16b08.r1 Stratagene lung (#937210) cDNA clone T63636.1 -- 3.550198352 -- IMAGE:80823 5' NM_000716.2 C4BPB 3.545953869 Complement component 4 binding protein, beta Complement and coagulation cascades(hsa04610) NM_005239.3 ETS2 3.540145048 v-ets erythroblastosis virus E26 oncogene homolog 2 (avian) -- Glycerophospholipid metabolism(hsa00564);;Glycine, serine and NM_005198.3 CPT1B 3.538394398 Carnitine palmitoyltransferase 1B (muscle) threonine metabolism(hsa00260);;Fatty acid NM_017617.2 NOTCH1 3.536770486 Notch homolog 1, translocation-associated (Drosophila) Notch signaling pathway(hsa04330) Endothelial differentiation, lysophosphatidic acid G-protein- BC036034.1 EDG2 3.527347078 Neuroactive ligand-receptor interaction(hsa04080) coupled receptor, 2 BU186365.1 FLJ20130 3.521450338 Hypothetical protein FLJ20130 -- NM_003255.2 TIMP2 3.492594977 tissue inhibitor of metalloproteinase 2 (TIMP2) -- SHC (Src homology 2 domain containing) transforming protein 1 NM_183001.2 SHC1 3.477854035 Focal adhesion(hsa04510) (SHC1) AI674189.1 -- 3.46418278 Homo sapiens, clone IMAGE:3832417, mRNA -- S100 calcium binding protein A4 (calcium protein, calvasculin, NM_002961.2 S100A4 3.463777861 -- metastasin, murine placental homolog) NM_005558.3 LAD1 3.448106979 Ladinin 1 -- NM_014854.1 SLC35E2 3.412606693 Solute carrier family 35, member E2 -- NM_138316.2 PANK1 3.400907825 Pantothenate kinase 1 Pantothenate and CoA biosynthesis(hsa00770) Transglutaminase 1 (K polypeptide epidermal type I, protein- NM_000359.1 TGM1 3.387636624 -- glutamine-gamma-glutamyltransferase) NM_138788.2 LOC120224 3.387280494 Hypothetical protein BC016153 -- NM_006017.1 PROM1 3.38163812 Prominin 1 -- NM_000153.1 GALC 3.362315064 Galactosylceramidase (Krabbe disease) Glycosphingolipid metabolism(hsa00600) NM_032262.1 DKFZp434N035 3.339481714 Hypothetical gene supported by AK094309 -- Sema domain, transmembrane domain (TM), and cytoplasmic NM_020796.2 SEMA6A 3.337687425 -- domain, (semaphorin) 6A UI-H-BW0-ajb-c-10-0-UIs1 NCI_CGAP_Sub6 cDNA clone AW296779.1 -- 3.332299742 -- IMAGE:2731027 3' Nuclear factor of kappa light polypeptide gene enhancer in B-cells Apoptosis(hsa04210);;Toll-like receptor signaling NM_020529.1 NFKBIA 3.317716971 inhibitor, alpha pathway(hsa04620) NM_145201.3 PP3856 3.288319385 Similar to CG3714 gene product -- BE904671.1 EPHA5 3.28664643 EPH receptor A5 -- MAPK signaling pathway(hsa04010);;Prostaglandin and AK093645.1 PLA2G2F 3.278620492 Phospholipase A2, group IIF leukotriene metabolism(hsa00590);;Glycerophospholipid NM_003879.3 CFLAR 3.275783807 CASP8 and FADD-like apoptosis regulator Apoptosis(hsa04210) NM_001049.2 SSTR1 3.26887196 Somatostatin receptor 1 Neuroactive ligand-receptor interaction(hsa04080) Calcium-binding tyrosine-(Y)-phosphorylation regulated NM_012189.2 CABYR 3.249321928 -- (fibrousheathin 2) AB011157.1 PTDSR 3.247777437 Phosphatidylserine receptor -- NM_007278.1 GABARAP 3.241577963 GABA(A) receptor-associated protein -- NM_144607.2 FLJ32499 3.233527279 Hypothetical protein FLJ32499 -- H86847.1 CXorf39 3.22800453 Chromosome X open reading frame 39 -- AW129281.1 GPX3 3.226934188 Glutathione peroxidase 3 (plasma) Glutathione metabolism(hsa00480) NM_052947.2 ALPK2 3.219877073 Alpha-kinase
Load more

Recommended publications
  • PARSANA-DISSERTATION-2020.Pdf
    DECIPHERING TRANSCRIPTIONAL PATTERNS OF GENE REGULATION: A COMPUTATIONAL APPROACH by Princy Parsana A dissertation submitted to The Johns Hopkins University in conformity with the requirements for the degree of Doctor of Philosophy Baltimore, Maryland July, 2020 © 2020 Princy Parsana All rights reserved Abstract With rapid advancements in sequencing technology, we now have the ability to sequence the entire human genome, and to quantify expression of tens of thousands of genes from hundreds of individuals. This provides an extraordinary opportunity to learn phenotype relevant genomic patterns that can improve our understanding of molecular and cellular processes underlying a trait. The high dimensional nature of genomic data presents a range of computational and statistical challenges. This dissertation presents a compilation of projects that were driven by the motivation to efficiently capture gene regulatory patterns in the human transcriptome, while addressing statistical and computational challenges that accompany this data. We attempt to address two major difficulties in this domain: a) artifacts and noise in transcriptomic data, andb) limited statistical power. First, we present our work on investigating the effect of artifactual variation in gene expression data and its impact on trans-eQTL discovery. Here we performed an in-depth analysis of diverse pre-recorded covariates and latent confounders to understand their contribution to heterogeneity in gene expression measurements. Next, we discovered 673 trans-eQTLs across 16 human tissues using v6 data from the Genotype Tissue Expression (GTEx) project. Finally, we characterized two trait-associated trans-eQTLs; one in Skeletal Muscle and another in Thyroid. Second, we present a principal component based residualization method to correct gene expression measurements prior to reconstruction of co-expression networks.
    [Show full text]
  • Structure and Function of the Fgd Family of Divergent FYVE Domain Proteins
    Biochemistry and Cell Biology Structure and Function of the Fgd Family of Divergent FYVE Domain Proteins Journal: Biochemistry and Cell Biology Manuscript ID bcb-2018-0185.R1 Manuscript Type: Mini Review Date Submitted by the 03-Aug-2018 Author: Complete List of Authors: Eitzen, Gary; University of Alberta Faculty of Medicine and Dentistry Smithers, Cameron C.; University of Alberta, Biochemistry Murray, Allan; University of Alberta Faculty of Medicine and Dentistry Overduin, Michael; University of Alberta Faculty of Medicine and Dentistry Draft Fgd, Pleckstrin Homology domain, FYVE domain, Dbl Homology Domain, Keyword: Rho GEF Is the invited manuscript for consideration in a Special CSMB Special Issue Issue? : https://mc06.manuscriptcentral.com/bcb-pubs Page 1 of 37 Biochemistry and Cell Biology Title: Structure and Function of the Fgd Family of Divergent FYVE Domain Proteins Authors: Gary Eitzen1, Cameron C. Smithers2, Allan G Murray3 and Michael Overduin2* Draft 1Department of Cell Biology, 2Department of Biochemistry, 3Department of Medicine, University of Alberta, Edmonton, Alberta, Canada *Corresponding author. Michael Overduin Telephone: +1 780 492 3518 Fax: +1 780 492-0886 E-mail: [email protected] https://mc06.manuscriptcentral.com/bcb-pubs Biochemistry and Cell Biology Page 2 of 37 Abstract FYVE domains are highly conserved protein modules that typically bind phosphatidylinositol 3-phosphate (PI3P) on the surface of early endosomes. Along with pleckstrin homology (PH) and phox homology (PX) domains, FYVE domains are the principal readers of the phosphoinositide (PI) code that mediate specific recognition of eukaryotic organelles. Of all the human FYVE domain-containing proteins, those within the Faciogenital dysplasia (Fgd) subfamily are particularly divergent, and couple with GTPases to exert unique cellular functions.
    [Show full text]
  • Establishing the Pathogenicity of Novel Mitochondrial DNA Sequence Variations: a Cell and Molecular Biology Approach
    Mafalda Rita Avó Bacalhau Establishing the Pathogenicity of Novel Mitochondrial DNA Sequence Variations: a Cell and Molecular Biology Approach Tese de doutoramento do Programa de Doutoramento em Ciências da Saúde, ramo de Ciências Biomédicas, orientada pela Professora Doutora Maria Manuela Monteiro Grazina e co-orientada pelo Professor Doutor Henrique Manuel Paixão dos Santos Girão e pela Professora Doutora Lee-Jun C. Wong e apresentada à Faculdade de Medicina da Universidade de Coimbra Julho 2017 Faculty of Medicine Establishing the pathogenicity of novel mitochondrial DNA sequence variations: a cell and molecular biology approach Mafalda Rita Avó Bacalhau Tese de doutoramento do programa em Ciências da Saúde, ramo de Ciências Biomédicas, realizada sob a orientação científica da Professora Doutora Maria Manuela Monteiro Grazina; e co-orientação do Professor Doutor Henrique Manuel Paixão dos Santos Girão e da Professora Doutora Lee-Jun C. Wong, apresentada à Faculdade de Medicina da Universidade de Coimbra. Julho, 2017 Copyright© Mafalda Bacalhau e Manuela Grazina, 2017 Esta cópia da tese é fornecida na condição de que quem a consulta reconhece que os direitos de autor são pertença do autor da tese e do orientador científico e que nenhuma citação ou informação obtida a partir dela pode ser publicada sem a referência apropriada e autorização. This copy of the thesis has been supplied on the condition that anyone who consults it recognizes that its copyright belongs to its author and scientific supervisor and that no quotation from the
    [Show full text]
  • Regulation of Cdc42 and Its Effectors in Epithelial Morphogenesis Franck Pichaud1,2,*, Rhian F
    © 2019. Published by The Company of Biologists Ltd | Journal of Cell Science (2019) 132, jcs217869. doi:10.1242/jcs.217869 REVIEW SUBJECT COLLECTION: ADHESION Regulation of Cdc42 and its effectors in epithelial morphogenesis Franck Pichaud1,2,*, Rhian F. Walther1 and Francisca Nunes de Almeida1 ABSTRACT An overview of Cdc42 Cdc42 – a member of the small Rho GTPase family – regulates cell Cdc42 was discovered in yeast and belongs to a large family of small – polarity across organisms from yeast to humans. It is an essential (20 30 kDa) GTP-binding proteins (Adams et al., 1990; Johnson regulator of polarized morphogenesis in epithelial cells, through and Pringle, 1990). It is part of the Ras-homologous Rho subfamily coordination of apical membrane morphogenesis, lumen formation and of GTPases, of which there are 20 members in humans, including junction maturation. In parallel, work in yeast and Caenorhabditis elegans the RhoA and Rac GTPases, (Hall, 2012). Rho, Rac and Cdc42 has provided important clues as to how this molecular switch can homologues are found in all eukaryotes, except for plants, which do generate and regulate polarity through localized activation or inhibition, not have a clear homologue for Cdc42. Together, the function of and cytoskeleton regulation. Recent studies have revealed how Rho GTPases influences most, if not all, cellular processes. important and complex these regulations can be during epithelial In the early 1990s, seminal work from Alan Hall and his morphogenesis. This complexity is mirrored by the fact that Cdc42 can collaborators identified Rho, Rac and Cdc42 as main regulators of exert its function through many effector proteins.
    [Show full text]
  • The Mineralocorticoid Receptor Leads to Increased Expression of EGFR
    www.nature.com/scientificreports OPEN The mineralocorticoid receptor leads to increased expression of EGFR and T‑type calcium channels that support HL‑1 cell hypertrophy Katharina Stroedecke1,2, Sandra Meinel1,2, Fritz Markwardt1, Udo Kloeckner1, Nicole Straetz1, Katja Quarch1, Barbara Schreier1, Michael Kopf1, Michael Gekle1 & Claudia Grossmann1* The EGF receptor (EGFR) has been extensively studied in tumor biology and recently a role in cardiovascular pathophysiology was suggested. The mineralocorticoid receptor (MR) is an important efector of the renin–angiotensin–aldosterone‑system and elicits pathophysiological efects in the cardiovascular system; however, the underlying molecular mechanisms are unclear. Our aim was to investigate the importance of EGFR for MR‑mediated cardiovascular pathophysiology because MR is known to induce EGFR expression. We identifed a SNP within the EGFR promoter that modulates MR‑induced EGFR expression. In RNA‑sequencing and qPCR experiments in heart tissue of EGFR KO and WT mice, changes in EGFR abundance led to diferential expression of cardiac ion channels, especially of the T‑type calcium channel CACNA1H. Accordingly, CACNA1H expression was increased in WT mice after in vivo MR activation by aldosterone but not in respective EGFR KO mice. Aldosterone‑ and EGF‑responsiveness of CACNA1H expression was confrmed in HL‑1 cells by Western blot and by measuring peak current density of T‑type calcium channels. Aldosterone‑induced CACNA1H protein expression could be abrogated by the EGFR inhibitor AG1478. Furthermore, inhibition of T‑type calcium channels with mibefradil or ML218 reduced diameter, volume and BNP levels in HL‑1 cells. In conclusion the MR regulates EGFR and CACNA1H expression, which has an efect on HL‑1 cell diameter, and the extent of this regulation seems to depend on the SNP‑216 (G/T) genotype.
    [Show full text]
  • How Macrophages Deal with Death
    REVIEWS CELL DEATH AND IMMUNITY How macrophages deal with death Greg Lemke Abstract | Tissue macrophages rapidly recognize and engulf apoptotic cells. These events require the display of so- called eat-me signals on the apoptotic cell surface, the most fundamental of which is phosphatidylserine (PtdSer). Externalization of this phospholipid is catalysed by scramblase enzymes, several of which are activated by caspase cleavage. PtdSer is detected both by macrophage receptors that bind to this phospholipid directly and by receptors that bind to a soluble bridging protein that is independently bound to PtdSer. Prominent among the latter receptors are the MER and AXL receptor tyrosine kinases. Eat-me signals also trigger macrophages to engulf virus- infected or metabolically traumatized, but still living, cells, and this ‘murder by phagocytosis’ may be a common phenomenon. Finally , the localized presentation of PtdSer and other eat- me signals on delimited cell surface domains may enable the phagocytic pruning of these ‘locally dead’ domains by macrophages, most notably by microglia of the central nervous system. In long- lived organisms, abundant cell types are often process. Efferocytosis is a remarkably efficient business: short- lived. In the human body, for example, the macrophages can engulf apoptotic cells in less than lifespan of many white blood cells — including neutro- 10 minutes, and it is therefore difficult experimentally to phils, eosinophils and platelets — is less than 2 weeks. detect free apoptotic cells in vivo, even in tissues where For normal healthy humans, a direct consequence of large numbers are generated7. Many of the molecules this turnover is the routine generation of more than that macrophages and other phagocytes use to recognize 100 billion dead cells each and every day of life1,2.
    [Show full text]
  • Two Locus Inheritance of Non-Syndromic Midline Craniosynostosis Via Rare SMAD6 and 4 Common BMP2 Alleles 5 6 Andrew T
    1 2 3 Two locus inheritance of non-syndromic midline craniosynostosis via rare SMAD6 and 4 common BMP2 alleles 5 6 Andrew T. Timberlake1-3, Jungmin Choi1,2, Samir Zaidi1,2, Qiongshi Lu4, Carol Nelson- 7 Williams1,2, Eric D. Brooks3, Kaya Bilguvar1,5, Irina Tikhonova5, Shrikant Mane1,5, Jenny F. 8 Yang3, Rajendra Sawh-Martinez3, Sarah Persing3, Elizabeth G. Zellner3, Erin Loring1,2,5, Carolyn 9 Chuang3, Amy Galm6, Peter W. Hashim3, Derek M. Steinbacher3, Michael L. DiLuna7, Charles 10 C. Duncan7, Kevin A. Pelphrey8, Hongyu Zhao4, John A. Persing3, Richard P. Lifton1,2,5,9 11 12 1Department of Genetics, Yale University School of Medicine, New Haven, CT, USA 13 2Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA 14 3Section of Plastic and Reconstructive Surgery, Department of Surgery, Yale University School of Medicine, New Haven, CT, USA 15 4Department of Biostatistics, Yale University School of Medicine, New Haven, CT, USA 16 5Yale Center for Genome Analysis, New Haven, CT, USA 17 6Craniosynostosis and Positional Plagiocephaly Support, New York, NY, USA 18 7Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, USA 19 8Child Study Center, Yale University School of Medicine, New Haven, CT, USA 20 9The Rockefeller University, New York, NY, USA 21 22 ABSTRACT 23 Premature fusion of the cranial sutures (craniosynostosis), affecting 1 in 2,000 24 newborns, is treated surgically in infancy to prevent adverse neurologic outcomes. To 25 identify mutations contributing to common non-syndromic midline (sagittal and metopic) 26 craniosynostosis, we performed exome sequencing of 132 parent-offspring trios and 59 27 additional probands.
    [Show full text]
  • Effect of a Caloric Restriction Based On
    UNIVERSIDAD AUTÓNOMA DE MADRID FACULTAD DE CIENCIAS DEPARTAMENTO DE BIOLOGÍA DOCTORAL THESIS Biology PhD “Effect of a caloric restriction based on the Mediterranean diet and intake of traditional Mediterranean foods on the expression of microRNAs regulating molecular processes associated with aging” INSTITUTO MADRILEÑO DE ESTUDIOS AVANZADOS EN ALIMENTACIÓN (IMDEA FOOD INSTITUTE) VÍCTOR MICÓ MORENO Madrid, 2018 UNIVERSIDAD AUTÓNOMA DE MADRID FACULTAD DE CIENCIAS DEPARTAMENTO DE BIOLOGÍA DOCTORAL THESIS Biology PhD “Effect of a caloric restriction based on the Mediterranean diet and intake of traditional Mediterranean foods on the expression of microRNAs regulating molecular processes associated with aging” INSTITUTO MADRILEÑO DE ESTUDIOS AVANZADOS EN ALIMENTACIÓN (IMDEA FOOD INSTITUTE) Memoria presentada por: Víctor Micó Moreno Para optar al grado de: DOCTOR EN BIOLOGÍA Doña Lidia Ángeles Daimiel Ruíz, Doctora en Biología Celular y Genética por la Universidad Autónoma de Madrid, investigadora del Instituto IMDEA Alimentación, informa favorablemente la solicitud de autorización de defensa de la tesis doctoral con el Título: “Effect of a caloric restriction based on the Mediterranean diet and intake of traditional Mediterranean foods on the expression of microRNAs regulating molecular processes associated with aging”, presentada por Don Víctor Micó Moreno para optar al grado de Doctor en Biología. Este trabajo ha sido realizado en el Instituto Madrileño de Estudios Avanzados en Alimentación (IMDEA Alimentación) bajo su dirección, y cumple satisfactoriamente las condiciones requeridas por el Departamento de Biología de la Universidad Autónoma de Madrid para optar al Título de Doctor. Ha actuado como tutor académico, y presenta su conformidad el Dr. Carlos Francisco Sentís Castaño, vicedecano de Personal Docente e Investigador y profesor titular del Departamento de Biología de la Facultad de Ciencias de la Universidad Autónoma de Madrid.
    [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]
  • Complement Component 4 Genes Contribute Sex-Specific Vulnerability in Diverse Illnesses
    bioRxiv preprint doi: https://doi.org/10.1101/761718; this version posted September 9, 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. Complement component 4 genes contribute sex-specific vulnerability in diverse illnesses Nolan Kamitaki1,2, Aswin Sekar1,2, Robert E. Handsaker1,2, Heather de Rivera1,2, Katherine Tooley1,2, David L. Morris3, Kimberly E. Taylor4, Christopher W. Whelan1,2, Philip Tombleson3, Loes M. Olde Loohuis5,6, Schizophrenia Working Group of the Psychiatric Genomics Consortium7, Michael Boehnke8, Robert P. Kimberly9, Kenneth M. Kaufman10, John B. Harley10, Carl D. Langefeld11, Christine E. Seidman1,12,13, Michele T. Pato14, Carlos N. Pato14, Roel A. Ophoff5,6, Robert R. Graham15, Lindsey A. Criswell4, Timothy J. Vyse3, Steven A. McCarroll1,2 1 Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA 2 Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA 3 Department of Medical and Molecular Genetics, King’s College London, London WC2R 2LS, UK 4 Rosalind Russell / Ephraim P Engleman Rheumatology Research Center, Division of Rheumatology, UCSF School of Medicine, San Francisco, California 94143, USA 5 Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA 6 Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California 90095, USA 7 A full list of collaborators is in Supplementary Information.
    [Show full text]
  • Investigation of Candidate Genes and Mechanisms Underlying Obesity
    Prashanth et al. BMC Endocrine Disorders (2021) 21:80 https://doi.org/10.1186/s12902-021-00718-5 RESEARCH ARTICLE Open Access Investigation of candidate genes and mechanisms underlying obesity associated type 2 diabetes mellitus using bioinformatics analysis and screening of small drug molecules G. Prashanth1 , Basavaraj Vastrad2 , Anandkumar Tengli3 , Chanabasayya Vastrad4* and Iranna Kotturshetti5 Abstract Background: Obesity associated type 2 diabetes mellitus is a metabolic disorder ; however, the etiology of obesity associated type 2 diabetes mellitus remains largely unknown. There is an urgent need to further broaden the understanding of the molecular mechanism associated in obesity associated type 2 diabetes mellitus. Methods: To screen the differentially expressed genes (DEGs) that might play essential roles in obesity associated type 2 diabetes mellitus, the publicly available expression profiling by high throughput sequencing data (GSE143319) was downloaded and screened for DEGs. Then, Gene Ontology (GO) and REACTOME pathway enrichment analysis were performed. The protein - protein interaction network, miRNA - target genes regulatory network and TF-target gene regulatory network were constructed and analyzed for identification of hub and target genes. The hub genes were validated by receiver operating characteristic (ROC) curve analysis and RT- PCR analysis. Finally, a molecular docking study was performed on over expressed proteins to predict the target small drug molecules. Results: A total of 820 DEGs were identified between
    [Show full text]
  • Noelia Díaz Blanco
    Effects of environmental factors on the gonadal transcriptome of European sea bass (Dicentrarchus labrax), juvenile growth and sex ratios Noelia Díaz Blanco Ph.D. thesis 2014 Submitted in partial fulfillment of the requirements for the Ph.D. degree from the Universitat Pompeu Fabra (UPF). This work has been carried out at the Group of Biology of Reproduction (GBR), at the Department of Renewable Marine Resources of the Institute of Marine Sciences (ICM-CSIC). Thesis supervisor: Dr. Francesc Piferrer Professor d’Investigació Institut de Ciències del Mar (ICM-CSIC) i ii A mis padres A Xavi iii iv Acknowledgements This thesis has been made possible by the support of many people who in one way or another, many times unknowingly, gave me the strength to overcome this "long and winding road". First of all, I would like to thank my supervisor, Dr. Francesc Piferrer, for his patience, guidance and wise advice throughout all this Ph.D. experience. But above all, for the trust he placed on me almost seven years ago when he offered me the opportunity to be part of his team. Thanks also for teaching me how to question always everything, for sharing with me your enthusiasm for science and for giving me the opportunity of learning from you by participating in many projects, collaborations and scientific meetings. I am also thankful to my colleagues (former and present Group of Biology of Reproduction members) for your support and encouragement throughout this journey. To the “exGBRs”, thanks for helping me with my first steps into this world. Working as an undergrad with you Dr.
    [Show full text]