DOCSLIB.ORG

Download Download

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Download Download Supplementary Fig S1. A network reconstructed from genes with three and more different intragenic SVA insertions. The initial networks, which were reconstructed automatically by IPA software, associated a number of highly linked genes (white blocks) to the uploaded dataset (dark red) and have been refined by deletion of the low-connected or redundant network nodes. Genes containing less than three SVA insertions are presented in pink. X-chromosome fragility gene FMR1 and the KRAB-family ZNF680 of genes are highlighted in blue and green, respectively. The meaning of the shapes is explained in the legend. Linked text labels correspond to gene-attributed functions and diseases. Solid lines reflect experimentally validated interactions and dashed lines correspond to indicative interactions (such as physical protein binding). Supplementary Fig S2. Anatomical gene expression heatmap produced by means of Genevestigator for neural system genes associated with SVA_A and/or SVA_B elements. Colour intensities correspond to the relative arithmetic mean of the detected level of expression of a gene (columns) in each listed tissue/cell type (rows). Supplementary Table S1. Genes with neuronal function and their corresponding SVA insertion location. Gene SVA-insertion location Up Entrez Entrez str Gene ID Gene ea Down Molecular for Entrez Gene ID ID for Symbol Entrez Gene Name Within m str. Location function Human for Mouse Rat Vesicle-Associated Vesicle Membrane Protein 1 VA membra VAMP1 (Synaptobrevin 1) -- MP1 -- ne other 6843 22317 25624 Fus fused in sarcoma Cytoplas FUS RNA binding protein -- FUS -- m other 2521 233908 317385 alanyl-tRNA synthetase 2, AAR Cytoplas AARS2 mitochondrial -- S2 -- m enzyme 57505 224805 301254 ATP-binding cassette, Plasma sub-family A (ABC1), Membra ABCA1 member 1 ABCA1 -- -- ne transporter 19 11303 313210 abhydrolase domain ABHD12 containing 12 ABHD12 -- -- Other enzyme 26090 76192 499913 ABL proto-oncogene 2, non-receptor Cytoplas ABL2 tyrosine kinase ABL2 -- -- m kinase 27 11352 304883 Plasma G-protein atypical chemokine CCB Membra coupled ACKR2 receptor 2 -- -- P2 ne receptor 1238 59289 140473 acyl-CoA thioesterase Cytoplas 100363 ACOT11 11 ACOT11 -- -- m enzyme 26027 329910 074 acyl-CoA synthetase long-chain family Cytoplas ACSL4 member 4 ACSL4 -- -- m enzyme 2182 50790 113976 ADAM Plasma metallopeptidase Membra ADAM19 domain 19 ADAM19 -- -- ne peptidase 8728 11492 303068 adenylate cyclase 10 ADC Cytoplas ADCY10 (soluble) -- -- Y10 m enzyme 55811 271639 59320 Plasma G-protein adhesion G protein- Membra coupled 100362 ADGRV1 coupled receptor V1 GPR98 -- -- ne receptor 84059 110789 255 adiponectin, C1Q and Extracell collagen domain ADI ular ADIPOQ containing -- -- POQ Space other 9370 11450 246253 Plasma G-protein Adenosine A3 Membra coupled 12193 ADORA3 Receptor ADORA3 -- -- ne receptor 3 562 25370 ATP/GTP binding AGTPBP1 protein 1 AGTPBP1 -- -- Nucleus peptidase 23287 67269 290986 Abelson helper Cytoplas AHI1 integration site 1 AHI1 -- -- m other 54806 52906 308923 aminoacyl tRNA synthetase complex- interacting Extracell multifunctional ular AIMP1 protein 1 AIMP1 -- -- Space cytokine 9255 13722 114632 aryl hydrocarbon receptor interacting transcriptio AIP protein -- AIP -- Nucleus n regulator 9049 11632 282827 A kinase (PRKA) AKAP9 anchor protein 9 AKAP9 -- -- Other other 10142 100986 246150 aldehyde dehydrogenase 7 Cytoplas ALDH7A1 family, member A1 ALDH7A1 -- -- m enzyme 501 110695 291450 arachidonate 5- Cytoplas ALOX5 lipoxygenase ALOX5 -- -- m enzyme 240 11689 25290 Plasma alkaline phosphatase, Membra phosphatas ALPL liver/bone/kidney -- ALPL -- ne e 249 11647 25586 Plasma Membra ANK2 ankyrin 2, neuronal ANK2 -- -- ne other 287 109676 362036 ankyrin repeat domain ANKRD11 11 ANKRD11 -- -- Nucleus other 29123 77087 365023 Plasma Membra ANXA2 annexin A2 ANXA2 -- -- ne other 302 12306 56611 apoptotic peptidase Cytoplas APAF1 activating factor 1 APAF1 -- -- m other 317 11783 78963 amyloid beta (A4) precursor protein- binding, family B, Cytoplas APBB2 member 2 APBB2 -- -- m other 323 11787 305338 amyloid beta (A4) precursor-like protein Cytoplas APLP2 2 APLP2 -- -- m other 334 11804 64312 Rho GTPase activating ARHGAP Cytoplas ARHGAP5 protein 5 5 -- -- m enzyme 394 11855 299012 ARH ARHGAP3 Rho GTPase activating GAP transcriptio 5 protein 35 -- -- 35 Nucleus n regulator 2909 232906 306400 Extracell ADP-ribosylation ular 20089 ARL13B factor-like 13B ARL13B -- -- Space other 4 68146 304037 aryl hydrocarbon receptor nuclear transcriptio ARNT translocator ARNT -- -- Nucleus n regulator 405 11863 25242 ASP Cytoplas ASPA aspartoacylase -- A -- m enzyme 443 11484 79251 activating ATF transcriptio ATF2 transcription factor 2 ATF2 -- 2 Nucleus n regulator 1386 11909 81647 Cytoplas ATG7 autophagy related 7 ATG7 -- -- m enzyme 10533 74244 312647 ATPase, Ca++ transporting, type 2C, Cytoplas ATP2C1 member 1 ATP2C1 -- -- m transporter 27032 235574 170699 ATPase, Cu++ Plasma transporting, alpha Membra ATP7A polypeptide ATP7A -- -- ne transporter 538 11977 24941 ATPase, aminophospholipid Plasma transporter, class I, Membra ATP8A2 type 8A, member 2 ATP8A2 -- -- ne transporter 51761 50769 691889 alpha thalassemia/mental retardation syndrome transcriptio ATRX X-linked ATRX -- -- Nucleus n regulator 546 22589 246284 ATX ATXN2 ataxin 2 ATXN2 -- N2 Nucleus other 6311 20239 288663 Bardet-Biedl Cytoplas 12988 BBS5 syndrome 5 BBS5 -- -- m other 0 72569 362142 Extracell Bardet-Biedl ular BBS9 syndrome 9 BBS9 -- -- Space other 27241 319845 315484 B-Raf proto-oncogene, serine/threonine Cytoplas BRAF kinase BRAF -- -- m enzyme 673 109880 114486 BRCA1-associated BRA 22192 BRAT1 ATM activator 1 -- -- T1 Nucleus other 7 231841 498150 breast cancer 1, early transcriptio BRCA1 onset BRCA1 -- -- Nucleus n regulator 672 12189 497672 bromodomain and WD repeat domain 25406 BRWD3 containing 3 BRWD3 -- -- Other other 5 382236 317213 Extracell complement ular C9 component 9 C9 -- -- Space other 735 12279 117512 C2 calcium-dependent Cytoplas C2CD3 domain containing 3 C2CD3 -- -- m other 26005 277939 293148 calcium channel, voltage-dependent, CAC Plasma CACNA2D alpha 2/delta subunit CACNA2 NA2 Membra 4 4 D4 D4 -- ne ion channel 93589 466912 312668 calcium channel, Plasma voltage-dependent, Membra CACNB4 beta 4 subunit CACNB4 -- -- ne ion channel 785 12298 58942 calcium/calmodulin- dependent protein Cytoplas CAMK1D kinase ID CAMK1D -- -- m kinase 57118 227541 307124 calmodulin binding transcription activator CAMTA1 1 CAMTA1 -- -- Other other 23261 100072 362665 calcium/calmodulin- dependent serine Plasma protein kinase Membra CASK (MAGUK family) CASK -- -- ne kinase 8573 12361 29647 caspase 6, apoptosis- related cysteine CAS Cytoplas CASP6 peptidase -- -- P6 m peptidase 839 12368 83584 caspase 8, apoptosis- related cysteine CAS CASP8 peptidase CASP8 -- P8 Nucleus peptidase 841 12370 64044 cerebral cavernous CCM Cytoplas CCM2 malformation 2 -- 2 -- m other 83605 216527 305505 CDK5 regulatory CDK5RAP subunit associated CDK5RAP Cytoplas 2 protein 2 2 -- -- m other 55755 214444 286919 cat eye syndrome chromosome region, CEC CECR2 candidate 2 -- -- R2 Nucleus other 27443 330409 500308 Extracell ular CFB complement factor B CFB -- -- Space peptidase 629 14962 294257 CASP8 and FADD-like CFL Cytoplas CFLAR apoptosis regulator CFLAR -- AR m other 8837 12633 117279 Plasma chloride channel, Membra CLCN3 voltage-sensitive 3 CLCN3 -- -- ne ion channel 1182 12725 84360 Plasma chloride intracellular CLIC Membra CLIC4 channel 4 CLIC4 4 -- ne ion channel 25932 29876 83718 ceroid-lipofuscinosis, neuronal 6, late Cytoplas CLN6 infantile, variant CLN6 -- -- m other 54982 76524 315746 Plasma Membra 15233 CNTN4 contactin 4 CNTN4 -- -- ne enzyme 0 269784 116658 Plasma contactin associated Membra CNTNAP2 protein-like 2 CNTNAP2 -- -- ne other 26047 66797 500105 Extracell ular CPA6 carboxypeptidase A6 CPA6 -- -- Space peptidase 57094 329093 312913 crumbs family member 1, photoreceptor Plasma morphogenesis Membra CRB1 associated CRB1 -- -- ne other 23418 170788 304825 cAMP responsive element binding CRE transcriptio CREB1 protein 1 -- -- B1 Nucleus n regulator 1385 12912 81646 CTS Cytoplas CTSS cathepsin S -- -- S m peptidase 1520 13040 50654 cytochrome P450, family 19, subfamily A, Cytoplas CYP19A1 polypeptide 1 CYP19A1 -- -- m enzyme 1588 13075 25147 cytochrome P450, family 7, subfamily B, Cytoplas CYP7B1 polypeptide 1 CYP7B1 -- -- m enzyme 9420 13123 25429 Plasma G-protein cysteinyl leukotriene CYSL Membra coupled CYSLTR1 receptor 1 -- -- TR1 ne receptor 10800 58861 114099 doublecortin-like DCLK1 kinase 1 DCLK1 -- -- Other kinase 9201 13175 83825 DNA-damage- DDI transcriptio DDIT3 inducible transcript 3 -- -- T3 Nucleus n regulator 1649 13198 29467 DIX domain containing DIX Cytoplas DIXDC1 1 -- -- DC1 m other 85458 330938 363062 DnaJ (Hsp40) homolog, subfamily C, Cytoplas 100360 DNAJC1 member 1 DNAJC1 -- -- m other 64215 13418 412 Plasma Membra DST dystonin DST -- -- ne other 667 13518 316313 Plasma Membra DYSF dysferlin DYSF -- -- ne other 8291 26903 312492 dyslexia susceptibility 16158 DYX1C1 1 candidate 1 DYX1C1 -- -- Nucleus other 2 67685 363096 ER degradation enhancer, mannosidase alpha- EDE Cytoplas EDEM2 like 2 -- M2 -- m enzyme 55741 108687 296304 eukaryotic translation initiation factor 2B, subunit 3 gamma, Cytoplas EIF2B3 58kDa EIF2B3 -- -- m other 8891 108067 171145 eukaryotic translation initiation factor 2B, EIF2 Cytoplas EIF2B4 subunit 4 delta, 67kDa -- -- B4 m other 8890 13667 117019 eukaryotic translation initiation factor 4 Cytoplas translation EIF4G3
Load more

Recommended publications
  • 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]
  • Constitutive Activation of RAS/MAPK Pathway Cooperates with Trisomy 21 and Is Therapeutically Exploitable in Down Syndrome B-Cell Leukemia
    Author Manuscript Published OnlineFirst on March 27, 2020; DOI: 10.1158/1078-0432.CCR-19-3519 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Constitutive activation of RAS/MAPK pathway cooperates with trisomy 21 and is therapeutically exploitable in Down syndrome B-cell Leukemia Anouchka P. Laurent1,2, Aurélie Siret1, Cathy Ignacimouttou1, Kunjal Panchal3, M’Boyba K. Diop4, Silvia Jenny5, Yi-Chien Tsai5, Damien Ross-Weil1, Zakia Aid1, Naïs Prade6, Stéphanie Lagarde6, Damien Plassard7, Gaelle Pierron8, Estelle Daudigeos-Dubus4, Yann Lecluse4, Nathalie Droin1, Beat Bornhauser5, Laurence C. Cheung3,9, John D. Crispino10, Muriel Gaudry1, Olivier A. Bernard1, Elizabeth Macintyre11, Carole Barin Bonnigal12, Rishi S. Kotecha3,9,13, Birgit Geoerger4, Paola Ballerini14, Jean-Pierre Bourquin5, Eric Delabesse6, Thomas Mercher1,15 and Sébastien Malinge1,3 1INSERM U1170, Gustave Roussy Institute, Université Paris Saclay, Villejuif, France 2Université Paris Diderot, Paris, France 3Telethon Kids Cancer Centre, Telethon Kids Institute, University of Western Australia, Perth, Australia 4Gustave Roussy Institute Cancer Campus, Department of Pediatric and Adolescent Oncology, INSERM U1015, Equipe Labellisée Ligue Nationale contre le Cancer, Université Paris-Saclay, Villejuif, France 5Department of Pediatric Oncology, Children’s Research Centre, University Children’s Hospital Zurich, Zurich, Switzerland 6Centre of Research on Cancer of Toulouse (CRCT), CHU Toulouse, Université Toulouse III, Toulouse, France 7IGBMC, Plateforme GenomEast, UMR7104 CNRS, Ilkirch, France 8Service de Génétique, Institut Curie, Paris, France 9School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Australia 10Division of Hematology/Oncology, Northwestern University, Chicago, USA 11Hematology, Université de Paris, Institut Necker-Enfants Malades and Assistance Publique – Hopitaux de Paris, Paris, France 12Centre Hospitalier Universitaire de Tours, Tours, France 1 Downloaded from clincancerres.aacrjournals.org on September 30, 2021.
    [Show full text]
  • Sex-Specific Hippocampal 5-Hydroxymethylcytosine Is Disrupted in Response to Acute Stress Ligia A
    University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Faculty Publications, Department of Statistics Statistics, Department of 2016 Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress Ligia A. Papale University of Wisconsin, [email protected] Sisi Li University of Wisconsin, [email protected] Andy Madrid University of Wisconsin, [email protected] Qi Zhang University of Nebraska-Lincoln, [email protected] Li Chen Emory University See next page for additional authors Follow this and additional works at: https://digitalcommons.unl.edu/statisticsfacpub Part of the Other Statistics and Probability Commons Papale, Ligia A.; Li, Sisi; Madrid, Andy; Zhang, Qi; Chen, Li; Chopra, Pankaj; Jin, Peng; Keles, Sunduz; and Alisch, Reid S., "Sex- specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress" (2016). Faculty Publications, Department of Statistics. 62. https://digitalcommons.unl.edu/statisticsfacpub/62 This Article is brought to you for free and open access by the Statistics, Department of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Faculty Publications, Department of Statistics by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Ligia A. Papale, Sisi Li, Andy Madrid, Qi Zhang, Li Chen, Pankaj Chopra, Peng Jin, Sunduz Keles, and Reid S. Alisch This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/statisticsfacpub/62 Neurobiology of Disease 96 (2016) 54–66 Contents lists available at ScienceDirect Neurobiology of Disease journal homepage: www.elsevier.com/locate/ynbdi Sex-specific hippocampal 5-hydroxymethylcytosine is disrupted in response to acute stress Ligia A. Papale a,1,SisiLia,c,1, Andy Madrid a,c,QiZhangd,LiChene,PankajChoprae,PengJine, Sündüz Keleş b, Reid S.
    [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]
  • Supplementary Table 3 Complete List of RNA-Sequencing Analysis of Gene Expression Changed by ≥ Tenfold Between Xenograft and Cells Cultured in 10%O2
    Supplementary Table 3 Complete list of RNA-Sequencing analysis of gene expression changed by ≥ tenfold between xenograft and cells cultured in 10%O2 Expr Log2 Ratio Symbol Entrez Gene Name (culture/xenograft) -7.182 PGM5 phosphoglucomutase 5 -6.883 GPBAR1 G protein-coupled bile acid receptor 1 -6.683 CPVL carboxypeptidase, vitellogenic like -6.398 MTMR9LP myotubularin related protein 9-like, pseudogene -6.131 SCN7A sodium voltage-gated channel alpha subunit 7 -6.115 POPDC2 popeye domain containing 2 -6.014 LGI1 leucine rich glioma inactivated 1 -5.86 SCN1A sodium voltage-gated channel alpha subunit 1 -5.713 C6 complement C6 -5.365 ANGPTL1 angiopoietin like 1 -5.327 TNN tenascin N -5.228 DHRS2 dehydrogenase/reductase 2 leucine rich repeat and fibronectin type III domain -5.115 LRFN2 containing 2 -5.076 FOXO6 forkhead box O6 -5.035 ETNPPL ethanolamine-phosphate phospho-lyase -4.993 MYO15A myosin XVA -4.972 IGF1 insulin like growth factor 1 -4.956 DLG2 discs large MAGUK scaffold protein 2 -4.86 SCML4 sex comb on midleg like 4 (Drosophila) Src homology 2 domain containing transforming -4.816 SHD protein D -4.764 PLP1 proteolipid protein 1 -4.764 TSPAN32 tetraspanin 32 -4.713 N4BP3 NEDD4 binding protein 3 -4.705 MYOC myocilin -4.646 CLEC3B C-type lectin domain family 3 member B -4.646 C7 complement C7 -4.62 TGM2 transglutaminase 2 -4.562 COL9A1 collagen type IX alpha 1 chain -4.55 SOSTDC1 sclerostin domain containing 1 -4.55 OGN osteoglycin -4.505 DAPL1 death associated protein like 1 -4.491 C10orf105 chromosome 10 open reading frame 105 -4.491
    [Show full text]
  • Emerging Roles for Multifunctional Ion Channel Auxiliary Subunits in Cancer T ⁎ Alexander S
    Cell Calcium 80 (2019) 125–140 Contents lists available at ScienceDirect Cell Calcium journal homepage: www.elsevier.com/locate/ceca Emerging roles for multifunctional ion channel auxiliary subunits in cancer T ⁎ Alexander S. Hawortha,b, William J. Brackenburya,b, a Department of Biology, University of York, Heslington, York, YO10 5DD, UK b York Biomedical Research Institute, University of York, Heslington, York, YO10 5DD, UK ARTICLE INFO ABSTRACT Keywords: Several superfamilies of plasma membrane channels which regulate transmembrane ion flux have also been Auxiliary subunit shown to regulate a multitude of cellular processes, including proliferation and migration. Ion channels are Cancer typically multimeric complexes consisting of conducting subunits and auxiliary, non-conducting subunits. Calcium channel Auxiliary subunits modulate the function of conducting subunits and have putative non-conducting roles, further Chloride channel expanding the repertoire of cellular processes governed by ion channel complexes to processes such as trans- Potassium channel cellular adhesion and gene transcription. Given this expansive influence of ion channels on cellular behaviour it Sodium channel is perhaps no surprise that aberrant ion channel expression is a common occurrence in cancer. This review will − focus on the conducting and non-conducting roles of the auxiliary subunits of various Ca2+,K+,Na+ and Cl channels and the burgeoning evidence linking such auxiliary subunits to cancer. Several subunits are upregu- lated (e.g. Cavβ,Cavγ) and downregulated (e.g. Kvβ) in cancer, while other subunits have been functionally implicated as oncogenes (e.g. Navβ1,Cavα2δ1) and tumour suppressor genes (e.g. CLCA2, KCNE2, BKγ1) based on in vivo studies. The strengthening link between ion channel auxiliary subunits and cancer has exposed these subunits as potential biomarkers and therapeutic targets.
    [Show full text]
  • Primate Specific Retrotransposons, Svas, in the Evolution of Networks That Alter Brain Function
    Title: Primate specific retrotransposons, SVAs, in the evolution of networks that alter brain function. Olga Vasieva1*, Sultan Cetiner1, Abigail Savage2, Gerald G. Schumann3, Vivien J Bubb2, John P Quinn2*, 1 Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, U.K 2 Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK 3 Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, D-63225 Germany *. Corresponding author Olga Vasieva: Institute of Integrative Biology, Department of Comparative genomics, University of Liverpool, Liverpool, L69 7ZB, [email protected] ; Tel: (+44) 151 795 4456; FAX:(+44) 151 795 4406 John Quinn: Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK, [email protected]; Tel: (+44) 151 794 5498. Key words: SVA, trans-mobilisation, behaviour, brain, evolution, psychiatric disorders 1 Abstract The hominid-specific non-LTR retrotransposon termed SINE–VNTR–Alu (SVA) is the youngest of the transposable elements in the human genome. The propagation of the most ancient SVA type A took place about 13.5 Myrs ago, and the youngest SVA types appeared in the human genome after the chimpanzee divergence. Functional enrichment analysis of genes associated with SVA insertions demonstrated their strong link to multiple ontological categories attributed to brain function and the disorders. SVA types that expanded their presence in the human genome at different stages of hominoid life history were also associated with progressively evolving behavioural features that indicated a potential impact of SVA propagation on a cognitive ability of a modern human.
    [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]
  • Mapping of Quantitative Trait Loci for Milk Yield Traits on Bovine Chromosome 5 in the Fleckvieh Cattle
    From the Department of Veterinary Sciences Faculty of Veterinary Medicine Ludwig-Maximilians-Universität München Arbeit angefertigt unter der Leitung von Univ. Prof. Dr. Dr. habil. Martin Förster Mapping of Quantitative Trait Loci for Milk Yield Traits on Bovine Chromosome 5 in the Fleckvieh Cattle Inaugural–Dissertation For the attainment of Doctor Degree in Veterinary Medicine From the Faculty of Veterinary Medicine of the Ludwig-Maximilians-Universität München by Ashraf Fathy Said Awad from Sharkia- Egypt München 2011 Gedruckt mit Genehmigung der Tierärztlichen Fakultät der Ludwig–Maximilians–Universität München Dekan: Univ. Prof. Dr. Braun Berichterstatter: Univ. Prof. Dr. Dr. habil Förster Korreferent: Univ. Prof. Dr. Mansfeld Tag der Promotion: 12. February 2011 This work is dedicated to My Parents, my wife and my lovely daughters; Sama, Shaza, Hana CONTENTS CONTENTS ABBREVIATION……………………………………………………………… IV CHAPTER 1: GENERAL INTRODUCTION……………………………….. 1 CHAPTER 2: REVIEW OF LITERATURE………………………………… 3 2.1. DNA Markers……………………………………………………….. 3 2.1.1. Microsatellites………………………………………………………….. 3 2.1.2. Single Nucleotide Polymorphism (SNPs)…………………………… 4 2.2. Mapping of Quantitative Trait Loci (QTL)…………………….. 5 2.2.1. QTL Mapping Designs………………………………………………... 6 2.2.1.1. Daughter Design………………………………………………... 6 2.2.1.2. Granddaughter Design………………………………………… 7 2.2.1.3. Complex Pedigree Design…………………………………….. 9 2.2.2. QTL Mapping Strategies……………………………………………… 10 2.2.2.1. Candidate Gene Approach……………………………………. 10 2.2.2.2. Genome Scan Approach……………………………………… 11 2.3. Principles of Linkage Mapping…………………………………. 12 2.4. QTL Fine Mapping………………………………………………… 14 2.4.1. Linkage Disequilibrium……………………………………………… 15 2.4.2. Combined Linkage Disequilibrium and Linkage (LDL) Mapping… 17 2.5. Identification of Candidate Genes……………………………… 18 2.6.
    [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]
  • Mitoxplorer, a Visual Data Mining Platform To
    mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations Annie Yim, Prasanna Koti, Adrien Bonnard, Fabio Marchiano, Milena Dürrbaum, Cecilia Garcia-Perez, José Villaveces, Salma Gamal, Giovanni Cardone, Fabiana Perocchi, et al. To cite this version: Annie Yim, Prasanna Koti, Adrien Bonnard, Fabio Marchiano, Milena Dürrbaum, et al.. mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dy- namics and mutations. Nucleic Acids Research, Oxford University Press, 2020, 10.1093/nar/gkz1128. hal-02394433 HAL Id: hal-02394433 https://hal-amu.archives-ouvertes.fr/hal-02394433 Submitted on 4 Dec 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License Nucleic Acids Research, 2019 1 doi: 10.1093/nar/gkz1128 Downloaded from https://academic.oup.com/nar/advance-article-abstract/doi/10.1093/nar/gkz1128/5651332 by Bibliothèque de l'université la Méditerranée user on 04 December 2019 mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations Annie Yim1,†, Prasanna Koti1,†, Adrien Bonnard2, Fabio Marchiano3, Milena Durrbaum¨ 1, Cecilia Garcia-Perez4, Jose Villaveces1, Salma Gamal1, Giovanni Cardone1, Fabiana Perocchi4, Zuzana Storchova1,5 and Bianca H.
    [Show full text]
  • A Genome-Wide Association Study Identifies Four Novel Susceptibility Loci Underlying Inguinal Hernia
    UCSF UC San Francisco Previously Published Works Title A genome-wide association study identifies four novel susceptibility loci underlying inguinal hernia. Permalink https://escholarship.org/uc/item/7g06z1k5 Journal Nature communications, 6(1) ISSN 2041-1723 Authors Jorgenson, Eric Makki, Nadja Shen, Ling et al. Publication Date 2015-12-21 DOI 10.1038/ncomms10130 Peer reviewed eScholarship.org Powered by the California Digital Library University of California ARTICLE Received 24 Aug 2015 | Accepted 6 Nov 2015 | Published 21 Dec 2015 DOI: 10.1038/ncomms10130 OPEN A genome-wide association study identifies four novel susceptibility loci underlying inguinal hernia Eric Jorgenson1,*, Nadja Makki2,3,*, Ling Shen1, David C. Chen4, Chao Tian5, Walter L. Eckalbar2,3, David Hinds5, Nadav Ahituv2,3 & Andrew Avins1 Inguinal hernia repair is one of the most commonly performed operations in the world, yet little is known about the genetic mechanisms that predispose individuals to develop inguinal hernias. We perform a genome-wide association analysis of surgically confirmed inguinal hernias in 72,805 subjects (5,295 cases and 67,510 controls) and confirm top associations in an independent cohort of 92,444 subjects with self-reported hernia repair surgeries (9,701 cases and 82,743 controls). We identify four novel inguinal hernia susceptibility loci in the regions of EFEMP1, WT1, EBF2 and ADAMTS6. Moreover, we observe expression of all four genes in mouse connective tissue and network analyses show an important role for two of these genes (EFEMP1 and WT1) in connective tissue maintenance/homoeostasis. Our findings provide insight into the aetiology of hernia development and highlight genetic pathways for studies of hernia development and its treatment.
    [Show full text]