DOCSLIB.ORG

Table S3 - List of 489 Non-Synonymous and Frame-Shifting Variants Which Were Predicted to Be Damaging (X: Termination Codon)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Table S3 - List of 489 Non-Synonymous and Frame-Shifting Variants Which Were Predicted to Be Damaging (X: Termination Codon) Table S3 - List of 489 non-synonymous and frame-shifting variants which were predicted to be damaging (X: termination codon). Gene Uniprot function Genome position (hg19) AA position & change SIFT Polyphen-2 Recognizes as substrates free retinal and cellular retinol-binding protein-bound retinal. Seems to be the key enzyme in the formation of an RA gradient chr15:101427859,c.287G>A(E3) p.96,R>H 0 1 ALDH1A3 along the dorso-ventral axis during the early eye development and also in the development of the olfactory system. chr15:101436180,c.709G>A(E7) p.237,G>R 0 0.99 IRAK3 Interleukin-1 receptor-associated kinase 3, Inhibits chr12:66605329,c.357C>A(E4), p.119, Y>X (417) _ _ dissociation of IRAK1 and IRAK4 from the Toll- like receptor signaling complex by either inhibiting the phosphorylation of IRAK1 and IRAK4 or stabilizing the receptor complex. Serine/threonine-protein kinase that acts as a molecular sensor for DNA damage. Involved in DNA non-homologous end joining (NHEJ) required for double-strand break (DSB) repair and V(D)J recombination. Must be bound to DNA to express its catalytic properties. Promotes processing of hairpin DNA structures in V(D)J recombination by activation of the hairpin endonuclease artemis (DCLRE1C). The assembly of the DNA-PK complex at DNA ends is also required for the NHEJ ligation step. Required to PRKDC protect and align broken ends of DNA. May also chr8:48697705,c.11075C>T(E77), p.3692, W>X(406) _ _ act as a scaffold protein to aid the localization of DNA repair proteins to the site of damage. Found at the ends of chromosomes, suggesting a further role in the maintenance of telomeric stability and the prevention of chromosomal end fusion. Also involved in modulation of transcription. Recognizes the substrate consensus sequence [ST]-Q. Phosphorylates 'Ser-139' of histone variant H2AX/H2AFX, thereby regulating DNA damage response mechanism. Phosphorylates DCLRE1C, c-Abl/ABL1, histone H1, HSPCA, c- Table S3 - List of 489 non-synonymous and frame-shifting variants which were predicted to be damaging (X: termination codon). Gene Uniprot function Genome position (hg19) AA position & change SIFT Polyphen-2 jun/JUN, p53/TP53, PARP1, POU2F1, DHX9, SRF, XRCC1, XRCC1, XRCC4, XRCC5, XRCC6, WRN, MYC and RFA2. Can phosphorylate C1D not only in the presence of linear DNA but also in the presence of supercoiled DNA. Ability to phosphorylate p53/TP53 in the presence of supercoiled DNA is dependent on C1D. Contributes to the determination of the circadian period length by antagonizing phosphorylation of CRY1 'Ser-588' and increasing CRY1 protein stability, most likely through an indirect machanism. Interacts with CRY1 and CRY2; negatively regulates CRY1 phosphorylation. Sodium channel protein type 2 subunit alpha, Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the SCN2A chr2:166245784 c.5468A>C(E27) p.1823,D>A 0.35 0.001 voltage difference across the membrane, the protein forms a sodium-selective channel through which Na+ ions may pass in accordance with their electrochemical gradient. Complement C4-A,Non-enzymatic component of C3 and C5 convertases and thus essential for the propagation of the classical complement pathway. Covalently binds to immunoglobulins and immune complexes and enhances the solubilization of immune aggregates and the clearance of IC through CR1 on erythrocytes. C4A isotype is C4A chr6:31964321 c.3620T>C(E28) p.1207,V>A 0.14 0 responsible for effective binding to form amide bonds with immune aggregates or protein antigens, while C4B isotype catalyzes the transacylation of the thioester carbonyl group to form ester bonds with carbohydrate antigens. Derived from proteolytic degradation of complement C4, C4a anaphylatoxin is a mediator Table S3 - List of 489 non-synonymous and frame-shifting variants which were predicted to be damaging (X: termination codon). Gene Uniprot function Genome position (hg19) AA position & change SIFT Polyphen-2 of local inflammatory process. It induces the contraction of smooth muscle, increases vascular permeability and causes histamine release from mast cells and basophilic leukocytes. Dynein heavy chain 11, axonemal, Force generating protein of respiratory cilia. Produces DNAH11 force towards the minus ends of microtubules. chr7:21658769 c.4321C>T(E24) p.1441,R>W _ 0.655 Dynein has ATPase activity; the force-producing power stroke is thought to occur on release of ADP. eIF-2-alpha kinase GCN2, Metabolic-stress sensing protein kinase that phosphorylates the alpha subunit of eukaryotic translation initiation factor 2 (eIF-2-alpha/EIF2S1) on 'Ser-52' in response to low amino acid availability (PubMed:25329545). Plays a role as an activator of the integrated stress response (ISR) required for adapatation to amino acid starvation. Converts phosphorylated eIF-2-alpha/EIF2S1 either to a competitive inhibitor of the translation initiation factor eIF-2B, leading to a global protein synthesis repression, and thus to a reduced overall utilization of amino acids, or to a translational initiation EIF2AK4 activation of specific mRNAs, such as the chr15:40284406 c.2662G>C(E17) p.888,D>H 0.28 0.33 transcriptional activator ATF4, and hence allowing ATF4-mediated reprogramming of amino acid biosynthetic gene expression to alleviate nutrient depletion. Binds uncharged tRNAs (By similarity). Involved in cell cycle arrest by promoting cyclin D1 mRNA translation repression after the unfolded protein response pathway (UPR) activation or cell cycle inhibitor CDKN1A/p21 mRNA translation activation in response to amino acid deprivation (PubMed:26102367). Plays a role in the consolidation of synaptic plasticity, learning as well as formation of long-term memory. Plays a role in neurite outgrowth inhibition. Plays a Table S3 - List of 489 non-synonymous and frame-shifting variants which were predicted to be damaging (X: termination codon). Gene Uniprot function Genome position (hg19) AA position & change SIFT Polyphen-2 proapoptotic role in response to glucose deprivation. Promotes global cellular protein synthesis repression in response to UV irradiation independently of the stress-activated protein kinase/c-Jun N-terminal kinase (SAPK/JNK) and p38 MAPK signaling pathways (By similarity). Plays a role in the antiviral response against alphavirus infection; impairs early viral mRNA translation of the incoming genomic virus RNA, thus preventing alphavirus replication (By similarity). Dynein regulatory complex protein 1, Key component of the nexin-dynein regulatory complex (N-DRC), essential for N-DRC integrity. Required for the assembly and regulation of CCDC164 chr2:26679362 c.2200G>A(E17) p.734,V>M 0.1 0.412 specific classes of inner dynein arm motors. May also function to restrict dynein-driven microtubule sliding, thus aiding in the generation of ciliary bending. Nephrocystin-4, Involved in the organization of apical junctions in kidney cells together with NPHP4 chr1:5987742 c.1408G>A(E11) p.470,R>W 0.09 0.742 NPHP1 and RPGRIP1L/NPHP8. Does not seem to be strictly required for ciliogenesis. Plasma kallikrein,The enzyme cleaves Lys-Arg and Arg-Ser bonds. It activates, in a reciprocal reaction, factor XII after its binding to a negatively KLKB1 charged surface. It also releases bradykinin from chr4:187171427 c.629C>A(E7) p.210,A>E 0.57 0.1 HMW kininogen and may also play a role in the renin-angiotensin system by converting prorenin into renin. Septin-12, Filament-forming cytoskeletal GTPase SEPT-12 (By similarity). May play a role in cytokinesis chr16:4837574 c.73C>T(E2) p.25,E>K 0.1 0.019 (Potential). Myotubularin-related protein 2, Phosphatase that MTMR2 acts on lipids with a phosphoinositol headgroup. chr11:95568581 c.1589G>C(E18) p.530,A>G 0.19 0.171 Has phosphatase activity towards Table S3 - List of 489 non-synonymous and frame-shifting variants which were predicted to be damaging (X: termination codon). Gene Uniprot function Genome position (hg19) AA position & change SIFT Polyphen-2 phosphatidylinositol 3-phosphate and phosphatidylinositol 3,5-bisphosphate. Nesprin-1,Multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain the subcellular spatial organization. Component of SUN-protein- containing multivariate complexes also called LINC complexes which link the nucleoskeleton and cytoskeleton by providing versatile outer SYNE1 nuclear membrane attachment sites for chr6:152652051 c.13556T>C(E77) p.4519,N>S _ 0.919 cytoskeletal filaments. May be involved in the maintenance of nuclear organization and structural integrity. Connects nuclei to the cytoskeleton by interacting with the nuclear envelope and with F- actin in the cytoplasm. May be required for centrosome migration to the apical cell surface during early ciliogenesis. WD repeat-containing protein 35, Component of the IFT complex A (IFT-A), a complex required for WDR35 retrograde ciliary transport. Required for chr2:20166621 c.1058C>G(E10) p.353,R>P 0.01 0.365 ciliogenesis. May promote CASP3 activation and TNF-stimulated apoptosis. Vitamin K epoxide reductase complex subunit 1,nvolved in vitamin K metabolism. Catalytic subunit of the vitamin K epoxide reductase (VKOR) complex which reduces inactive vitamin VKORC1 K 2,3-epoxide to active vitamin K. Vitamin K is chr16:31104713 c.203T>C(E2) p.68,H>R 0.37 0.03 required for the gamma-carboxylation of various proteins, including clotting factors, and is required for normal blood coagulation, but also for normal bone development. Dihydropyrimidine dehydrogenase [NADP(+)], Involved in pyrimidine base degradation. DPYD Catalyzes the reduction of uracil and thymine. chr1:97700547 c.2303G>T(E19) p.768,T>K 0.16 0.046 Also involved the degradation of the chemotherapeutic drug 5-fluorouracil. Table S3 - List of 489 non-synonymous and frame-shifting variants which were predicted to be damaging (X: termination codon). Gene Uniprot function Genome position (hg19) AA position & change SIFT Polyphen-2 USH2A Usherin,Involved in hearing and vision.
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]
  • Cooperativity of Imprinted Genes Inactivated by Acquired Chromosome 20Q Deletions
    Cooperativity of imprinted genes inactivated by acquired chromosome 20q deletions Athar Aziz, … , Anne C. Ferguson-Smith, Anthony R. Green J Clin Invest. 2013;123(5):2169-2182. https://doi.org/10.1172/JCI66113. Research Article Oncology Large regions of recurrent genomic loss are common in cancers; however, with a few well-characterized exceptions, how they contribute to tumor pathogenesis remains largely obscure. Here we identified primate-restricted imprinting of a gene cluster on chromosome 20 in the region commonly deleted in chronic myeloid malignancies. We showed that a single heterozygous 20q deletion consistently resulted in the complete loss of expression of the imprinted genes L3MBTL1 and SGK2, indicative of a pathogenetic role for loss of the active paternally inherited locus. Concomitant loss of both L3MBTL1 and SGK2 dysregulated erythropoiesis and megakaryopoiesis, 2 lineages commonly affected in chronic myeloid malignancies, with distinct consequences in each lineage. We demonstrated that L3MBTL1 and SGK2 collaborated in the transcriptional regulation of MYC by influencing different aspects of chromatin structure. L3MBTL1 is known to regulate nucleosomal compaction, and we here showed that SGK2 inactivated BRG1, a key ATP-dependent helicase within the SWI/SNF complex that regulates nucleosomal positioning. These results demonstrate a link between an imprinted gene cluster and malignancy, reveal a new pathogenetic mechanism associated with acquired regions of genomic loss, and underline the complex molecular and cellular consequences of “simple” cancer-associated chromosome deletions. Find the latest version: https://jci.me/66113/pdf Research article Cooperativity of imprinted genes inactivated by acquired chromosome 20q deletions Athar Aziz,1,2 E. Joanna Baxter,1,2,3 Carol Edwards,4 Clara Yujing Cheong,5 Mitsuteru Ito,4 Anthony Bench,3 Rebecca Kelley,1,2 Yvonne Silber,1,2 Philip A.
    [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]
  • MUC4/MUC16/Muc20high Signature As a Marker of Poor Prognostic for Pancreatic, Colon and Stomach Cancers
    Jonckheere and Van Seuningen J Transl Med (2018) 16:259 https://doi.org/10.1186/s12967-018-1632-2 Journal of Translational Medicine RESEARCH Open Access Integrative analysis of the cancer genome atlas and cancer cell lines encyclopedia large‑scale genomic databases: MUC4/MUC16/ MUC20 signature is associated with poor survival in human carcinomas Nicolas Jonckheere* and Isabelle Van Seuningen* Abstract Background: MUC4 is a membrane-bound mucin that promotes carcinogenetic progression and is often proposed as a promising biomarker for various carcinomas. In this manuscript, we analyzed large scale genomic datasets in order to evaluate MUC4 expression, identify genes that are correlated with MUC4 and propose new signatures as a prognostic marker of epithelial cancers. Methods: Using cBioportal or SurvExpress tools, we studied MUC4 expression in large-scale genomic public datasets of human cancer (the cancer genome atlas, TCGA) and cancer cell line encyclopedia (CCLE). Results: We identifed 187 co-expressed genes for which the expression is correlated with MUC4 expression. Gene ontology analysis showed they are notably involved in cell adhesion, cell–cell junctions, glycosylation and cell signal- ing. In addition, we showed that MUC4 expression is correlated with MUC16 and MUC20, two other membrane-bound mucins. We showed that MUC4 expression is associated with a poorer overall survival in TCGA cancers with diferent localizations including pancreatic cancer, bladder cancer, colon cancer, lung adenocarcinoma, lung squamous adeno- carcinoma, skin cancer and stomach cancer. We showed that the combination of MUC4, MUC16 and MUC20 signature is associated with statistically signifcant reduced overall survival and increased hazard ratio in pancreatic, colon and stomach cancer.
    [Show full text]
  • Genome-Wide Parent-Of-Origin DNA Methylation Analysis Reveals The
    Downloaded from genome.cshlp.org on September 25, 2021 - Published by Cold Spring Harbor Laboratory Press Research Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment Franck Court,1,15 Chiharu Tayama,2,15 Valeria Romanelli,1,15 Alex Martin-Trujillo,1,15 Isabel Iglesias-Platas,3 Kohji Okamura,4 Naoko Sugahara,2 Carlos Simo´n,5 Harry Moore,6 Julie V. Harness,7 Hans Keirstead,7 Jose Vicente Sanchez-Mut,8 Eisuke Kaneki,9 Pablo Lapunzina,10 Hidenobu Soejima,11 Norio Wake,9 Manel Esteller,8,12,13 Tsutomu Ogata,14 Kenichiro Hata,2 Kazuhiko Nakabayashi,2,16,17 and David Monk1,16,17 1–14[Author affiliations appear at the end of the paper.] Differential methylation between the two alleles of a gene has been observed in imprinted regions, where the methylation of one allele occurs on a parent-of-origin basis, the inactive X-chromosome in females, and at those loci whose methylation is driven by genetic variants. We have extensively characterized imprinted methylation in a substantial range of normal human tissues, reciprocal genome-wide uniparental disomies, and hydatidiform moles, using a combination of whole- genome bisulfite sequencing and high-density methylation microarrays. This approach allowed us to define methylation profiles at known imprinted domains at base-pair resolution, as well as to identify 21 novel loci harboring parent-of-origin methylation, 15 of which are restricted to the placenta. We observe that the extent of imprinted differentially methylated regions (DMRs) is extremely similar between tissues, with the exception of the placenta.
    [Show full text]
  • Transcriptional Control of Tissue-Resident Memory T Cell Generation
    Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2019 © 2019 Filip Cvetkovski All rights reserved ABSTRACT Transcriptional control of tissue-resident memory T cell generation Filip Cvetkovski Tissue-resident memory T cells (TRM) are a non-circulating subset of memory that are maintained at sites of pathogen entry and mediate optimal protection against reinfection. Lung TRM can be generated in response to respiratory infection or vaccination, however, the molecular pathways involved in CD4+TRM establishment have not been defined. Here, we performed transcriptional profiling of influenza-specific lung CD4+TRM following influenza infection to identify pathways implicated in CD4+TRM generation and homeostasis. Lung CD4+TRM displayed a unique transcriptional profile distinct from spleen memory, including up-regulation of a gene network induced by the transcription factor IRF4, a known regulator of effector T cell differentiation. In addition, the gene expression profile of lung CD4+TRM was enriched in gene sets previously described in tissue-resident regulatory T cells. Up-regulation of immunomodulatory molecules such as CTLA-4, PD-1, and ICOS, suggested a potential regulatory role for CD4+TRM in tissues. Using loss-of-function genetic experiments in mice, we demonstrate that IRF4 is required for the generation of lung-localized pathogen-specific effector CD4+T cells during acute influenza infection. Influenza-specific IRF4−/− T cells failed to fully express CD44, and maintained high levels of CD62L compared to wild type, suggesting a defect in complete differentiation into lung-tropic effector T cells.
    [Show full text]
  • Downloaded from [266]
    Patterns of DNA methylation on the human X chromosome and use in analyzing X-chromosome inactivation by Allison Marie Cotton B.Sc., The University of Guelph, 2005 A THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in The Faculty of Graduate Studies (Medical Genetics) THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver) January 2012 © Allison Marie Cotton, 2012 Abstract The process of X-chromosome inactivation achieves dosage compensation between mammalian males and females. In females one X chromosome is transcriptionally silenced through a variety of epigenetic modifications including DNA methylation. Most X-linked genes are subject to X-chromosome inactivation and only expressed from the active X chromosome. On the inactive X chromosome, the CpG island promoters of genes subject to X-chromosome inactivation are methylated in their promoter regions, while genes which escape from X- chromosome inactivation have unmethylated CpG island promoters on both the active and inactive X chromosomes. The first objective of this thesis was to determine if the DNA methylation of CpG island promoters could be used to accurately predict X chromosome inactivation status. The second objective was to use DNA methylation to predict X-chromosome inactivation status in a variety of tissues. A comparison of blood, muscle, kidney and neural tissues revealed tissue-specific X-chromosome inactivation, in which 12% of genes escaped from X-chromosome inactivation in some, but not all, tissues. X-linked DNA methylation analysis of placental tissues predicted four times higher escape from X-chromosome inactivation than in any other tissue. Despite the hypomethylation of repetitive elements on both the X chromosome and the autosomes, no changes were detected in the frequency or intensity of placental Cot-1 holes.
    [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]
  • Supplementary Table 1: Adhesion Genes Data Set
    Supplementary Table 1: Adhesion genes data set PROBE Entrez Gene ID Celera Gene ID Gene_Symbol Gene_Name 160832 1 hCG201364.3 A1BG alpha-1-B glycoprotein 223658 1 hCG201364.3 A1BG alpha-1-B glycoprotein 212988 102 hCG40040.3 ADAM10 ADAM metallopeptidase domain 10 133411 4185 hCG28232.2 ADAM11 ADAM metallopeptidase domain 11 110695 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 195222 8038 hCG40937.4 ADAM12 ADAM metallopeptidase domain 12 (meltrin alpha) 165344 8751 hCG20021.3 ADAM15 ADAM metallopeptidase domain 15 (metargidin) 189065 6868 null ADAM17 ADAM metallopeptidase domain 17 (tumor necrosis factor, alpha, converting enzyme) 108119 8728 hCG15398.4 ADAM19 ADAM metallopeptidase domain 19 (meltrin beta) 117763 8748 hCG20675.3 ADAM20 ADAM metallopeptidase domain 20 126448 8747 hCG1785634.2 ADAM21 ADAM metallopeptidase domain 21 208981 8747 hCG1785634.2|hCG2042897 ADAM21 ADAM metallopeptidase domain 21 180903 53616 hCG17212.4 ADAM22 ADAM metallopeptidase domain 22 177272 8745 hCG1811623.1 ADAM23 ADAM metallopeptidase domain 23 102384 10863 hCG1818505.1 ADAM28 ADAM metallopeptidase domain 28 119968 11086 hCG1786734.2 ADAM29 ADAM metallopeptidase domain 29 205542 11085 hCG1997196.1 ADAM30 ADAM metallopeptidase domain 30 148417 80332 hCG39255.4 ADAM33 ADAM metallopeptidase domain 33 140492 8756 hCG1789002.2 ADAM7 ADAM metallopeptidase domain 7 122603 101 hCG1816947.1 ADAM8 ADAM metallopeptidase domain 8 183965 8754 hCG1996391 ADAM9 ADAM metallopeptidase domain 9 (meltrin gamma) 129974 27299 hCG15447.3 ADAMDEC1 ADAM-like,
    [Show full text]
  • Imprinting of the Human L3MBTL Gene, a Polycomb Family Member Located in a Region of Chromosome 20 Deleted in Human Myeloid Malignancies
    Correction GENETICS Correction for “Imprinting of the human L3MBTL gene, a poly- The authors note that a mistake occurred during the prepa- comb family member located in a region of chromosome 20 deleted ration of Fig. 1B. Three control lanes (6, 7, and 8) were inad- in human myeloid malignancies,” by Juan Li, Anthony J. Bench, vertently duplicated and also shown as lanes 3, 4, and 5. This George S. Vassiliou, Nasios Fourouclas, Anne C. Ferguson-Smith, resulted from a technical error during preparation of the figure and Anthony R. Green, first published April 30, 2004; 10.1073/ and does not alter any of the conclusions of the paper. The pnas.0308195101 (Proc. Natl. Acad. Sci. U.S.A. 101, 7341–7346). corrected figure and the unaltered figure legend appear below. A CORRECTION B C Fig. 1. Allelic methylation of the L3MBTL gene. (A) Locus of the L3MBTL gene and intron/exon structure of its 5′ and 3′ regions. Coding and noncoding exons are shown in black and gray boxes, respectively. Bent arrows indicate two putative promoters. Patterned horizontal bars represent the four CpG islands. Asterisks indicate the locations of SNPs used in the study, and primers spanning the respective SNPs are indicated (P1–P8). (B) Methylation analysis of the CpG island 3 by using SSCP. Lane 1, universally methylated genomic control DNA; lanes 2–5, normal bone marrow; lanes 6–9, normal granulocytes; lanes 10–13, granulocytes from patients, with an acquired 20q deletion. (C) Bisulfite sequencing of CpG island 3. Sequences relate to samples corresponding to individual lanes from B, as indicated.
    [Show full text]
  • The Role of Regulated Necrosis in Endocrine Diseases
    PERSPECTIVES system results in the typical morphological features such as rapid shrinking of the cell, The role of regulated necrosis nuclear condensation, DNA fragmentation, exposure of phosphatidylserine and a in endocrine diseases process known as membrane blebbing11,12. Phosphatidylserine exposure functions Wulf Tonnus , Alexia Belavgeni , Felix Beuschlein , Graeme Eisenhofer, as an ‘eat me’ signal to macrophages13–15. Martin Fassnacht , Matthias Kroiss , Nils P. Krone, Martin Reincke , Importantly, the plasma membrane remains intact in apoptotically dying cells, Stefan R. Bornstein and Andreas Linkermann a mechanism that prevents the release of Abstract | The death of endocrine cells is involved in type 1 diabetes mellitus, intracellular content to the interstitial and/or autoimmunity, adrenopause and hypogonadotropism. Insights from research on extracellular space. Therefore, apoptosis is immunologically silent. The detection basic cell death have revealed that most pathophysiologically important cell death of apoptosis has been misinterpreted for is necrotic in nature, whereas regular metabolism is maintained by apoptosis decades by the TdT-mediated dUTP-biotin programmes. Necrosis is defined as cell death by plasma membrane rupture, which nick end- labelling (TUNEL) method (BOx 1). allows the release of damage- associated molecular patterns that trigger an Mechanistically, extrinsic apoptosis immune response referred to as necroinflammation. Regulated necrosis comes in is mediated by death receptors such as different forms, such as necroptosis, pyroptosis and ferroptosis. In this Perspective, tumour necrosis factor receptor 1 (TNFR1) or the FAS receptor (also known as with a focus on the endocrine environment, we introduce these cell death CD95)16. To kill a cell through a TNFR1 pathways and discuss the specific consequences of regulated necrosis.
    [Show full text]
  • Relating Metatranscriptomic Profiles to the Micropollutant
    1 Relating Metatranscriptomic Profiles to the 2 Micropollutant Biotransformation Potential of 3 Complex Microbial Communities 4 5 Supporting Information 6 7 Stefan Achermann,1,2 Cresten B. Mansfeldt,1 Marcel Müller,1,3 David R. Johnson,1 Kathrin 8 Fenner*,1,2,4 9 1Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, 10 Switzerland. 2Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, 8092 11 Zürich, Switzerland. 3Institute of Atmospheric and Climate Science, ETH Zürich, 8092 12 Zürich, Switzerland. 4Department of Chemistry, University of Zürich, 8057 Zürich, 13 Switzerland. 14 *Corresponding author (email: [email protected] ) 15 S.A and C.B.M contributed equally to this work. 16 17 18 19 20 21 This supporting information (SI) is organized in 4 sections (S1-S4) with a total of 10 pages and 22 comprises 7 figures (Figure S1-S7) and 4 tables (Table S1-S4). 23 24 25 S1 26 S1 Data normalization 27 28 29 30 Figure S1. Relative fractions of gene transcripts originating from eukaryotes and bacteria. 31 32 33 Table S1. Relative standard deviation (RSD) for commonly used reference genes across all 34 samples (n=12). EC number mean fraction bacteria (%) RSD (%) RSD bacteria (%) RSD eukaryotes (%) 2.7.7.6 (RNAP) 80 16 6 nda 5.99.1.2 (DNA topoisomerase) 90 11 9 nda 5.99.1.3 (DNA gyrase) 92 16 10 nda 1.2.1.12 (GAPDH) 37 39 6 32 35 and indicates not determined. 36 37 38 39 S2 40 S2 Nitrile hydration 41 42 43 44 Figure S2: Pearson correlation coefficients r for rate constants of bromoxynil and acetamiprid with 45 gene transcripts of ECs describing nucleophilic reactions of water with nitriles.
    [Show full text]