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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. -
Myopathy Genes (HGNC) Neuropathy (HGNC) Neuromuscular Disease
Myopathy Genes Neuropathy Neuromuscular Disease (HGNC) (HGNC) (HGNC) ABHD5 ABCA1 ADCK3 ACTG2 ACO2 AGRN AGK AGXT ALS2 ALDOA AIFM1 ANG AMER1 ALAD AP4B1 ANO5 AMACR AP4E1 AR AP1S1 AP4M1 AUH APTX AP4S1 B4GALT1 AR AP5Z1 CACNA1S ATL3 ATM CASQ1 B4GALNT1 ATXN10 CCDC78 BAG3 ATXN7 CHCHD10 BRP44L BEAN1 CHRNA1 C12orf65 C9orf72 CHRNB1 C19orf12 CACNB4 CHRND C1NH CAPN3 CHRNE CECR1 CHAT CLPB CISD2 CHKB COL6A1 CLCF1 CHMP2B COL6A2 CLCN2 CHRNG COL6A3 CLP1 CLCN1 COLQ CMT2G COL9A3 CTNS CMT2H COQ2 DGUOK CMTDIA COQ6 DNA2 CMTX2 COQ9 DNAJB6 CMTX3 COX15 DNAJC19 COASY CPT1A DNM2 COX6A1 CYP7B1 DPM2 CPOX DAG1 DYSF CYP27A1 DDHD2 EMD CYP2U1 DOK7 EPG5 DARS2 DPAGT1 FAM111B DCAF8 DPM3 FBXL4 DDHD1 DUX4 FKBP14 DFNX5 ECEL1 FKRP DHTKD1 ERBB3 FLH1 DIAPH3 ERLIN2 FLNC DNAJB2 FA2H HNRNPA1 DNAJC3 FKTN HNRNPDL ELOVL5 FUS HNRPA2B1 ERCC8 G6PC KLHL40 FAH GFPT1 KLHL41 FAM126A GLE1 LAMA2 FBN1 GYS2 LDB3 FMR1 HSPD1 LMOD3 FXN IFRD1 MEGF10 GALC INF2 MGME1 GBE1 ISPD MTAP GJC2 ITGA7 MTMR14 GP1BA ITPR1 MYF6 HADHA KCNA1 MYH14 HADHB KCNC3 MYLK2 HFE KCNE3 NARS2 HINT1 KCNJ18 NEB HK1 KCNJ2 ORAI1 HMBS KIAA0196 PRKAG2 HSD17B4 KIF21A PTEN HSN1B L1CAM RBCK1 IARS2 LAMB2 RET IGHMBP2 LARGE RMND1 KCNJ10 MCCC2 SCN4A KIF5A MRE11A SERAC1 LRSAM1 MRPL3 SGCA LYST MTO1 SIL1 MANBA MTPAP SPEG MARS MTTP STAC3 MTATP6 MUSK STIM1 MYH14 MYBPC3 SYNE1 MYOT MYH3 SYNE2 NAMSD MYH8 TAZ NF2 NF1 TIA1 NGLY1 NIPA1 TMEM43 NMSR NOP56 TNPO3 NOTCH3 OPTN TNXB OPA1 PDSS2 TPM2 OPA3 PDYN TRPV4 OTOF PFN1 UBA1 PDK3 PHKA2 VCP PDSS1 PHKG2 XDH PEX10 PHOX2A ACADS PEX2 PIP5K1C ACADVL PMM2 PLEC ACTA1 PNPLA6 PLP1 AGL PPOX POMGNT1 AMPD1 PRICKLE1 -
Supplementary Table 2
Supplementary Table 2. Differentially Expressed Genes following Sham treatment relative to Untreated Controls Fold Change Accession Name Symbol 3 h 12 h NM_013121 CD28 antigen Cd28 12.82 BG665360 FMS-like tyrosine kinase 1 Flt1 9.63 NM_012701 Adrenergic receptor, beta 1 Adrb1 8.24 0.46 U20796 Nuclear receptor subfamily 1, group D, member 2 Nr1d2 7.22 NM_017116 Calpain 2 Capn2 6.41 BE097282 Guanine nucleotide binding protein, alpha 12 Gna12 6.21 NM_053328 Basic helix-loop-helix domain containing, class B2 Bhlhb2 5.79 NM_053831 Guanylate cyclase 2f Gucy2f 5.71 AW251703 Tumor necrosis factor receptor superfamily, member 12a Tnfrsf12a 5.57 NM_021691 Twist homolog 2 (Drosophila) Twist2 5.42 NM_133550 Fc receptor, IgE, low affinity II, alpha polypeptide Fcer2a 4.93 NM_031120 Signal sequence receptor, gamma Ssr3 4.84 NM_053544 Secreted frizzled-related protein 4 Sfrp4 4.73 NM_053910 Pleckstrin homology, Sec7 and coiled/coil domains 1 Pscd1 4.69 BE113233 Suppressor of cytokine signaling 2 Socs2 4.68 NM_053949 Potassium voltage-gated channel, subfamily H (eag- Kcnh2 4.60 related), member 2 NM_017305 Glutamate cysteine ligase, modifier subunit Gclm 4.59 NM_017309 Protein phospatase 3, regulatory subunit B, alpha Ppp3r1 4.54 isoform,type 1 NM_012765 5-hydroxytryptamine (serotonin) receptor 2C Htr2c 4.46 NM_017218 V-erb-b2 erythroblastic leukemia viral oncogene homolog Erbb3 4.42 3 (avian) AW918369 Zinc finger protein 191 Zfp191 4.38 NM_031034 Guanine nucleotide binding protein, alpha 12 Gna12 4.38 NM_017020 Interleukin 6 receptor Il6r 4.37 AJ002942 -
A Genome-Wide Screen in Mice to Identify Cell-Extrinsic Regulators of Pulmonary Metastatic Colonisation
FEATURED ARTICLE MUTANT SCREEN REPORT A Genome-Wide Screen in Mice To Identify Cell-Extrinsic Regulators of Pulmonary Metastatic Colonisation Louise van der Weyden,1 Agnieszka Swiatkowska, Vivek Iyer, Anneliese O. Speak, and David J. Adams Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom ORCID IDs: 0000-0002-0645-1879 (L.v.d.W.); 0000-0003-4890-4685 (A.O.S.); 0000-0001-9490-0306 (D.J.A.) ABSTRACT Metastatic colonization, whereby a disseminated tumor cell is able to survive and proliferate at a KEYWORDS secondary site, involves both tumor cell-intrinsic and -extrinsic factors. To identify tumor cell-extrinsic metastasis (microenvironmental) factors that regulate the ability of metastatic tumor cells to effectively colonize a metastatic tissue, we performed a genome-wide screen utilizing the experimental metastasis assay on mutant mice. colonisation Mutant and wildtype (control) mice were tail vein-dosed with murine metastatic melanoma B16-F10 cells and microenvironment 10 days later the number of pulmonary metastatic colonies were counted. Of the 1,300 genes/genetic B16-F10 locations (1,344 alleles) assessed in the screen 34 genes were determined to significantly regulate pulmonary lung metastatic colonization (15 increased and 19 decreased; P , 0.005 and genotype effect ,-55 or .+55). mutant While several of these genes have known roles in immune system regulation (Bach2, Cyba, Cybb, Cybc1, Id2, mouse Igh-6, Irf1, Irf7, Ncf1, Ncf2, Ncf4 and Pik3cg) most are involved in a disparate range of biological processes, ranging from ubiquitination (Herc1) to diphthamide synthesis (Dph6) to Rho GTPase-activation (Arhgap30 and Fgd4), with no previous reports of a role in the regulation of metastasis. -
Rho Guanine Nucleotide Exchange Factors: Regulators of Rho Gtpase Activity in Development and Disease
Oncogene (2014) 33, 4021–4035 & 2014 Macmillan Publishers Limited All rights reserved 0950-9232/14 www.nature.com/onc REVIEW Rho guanine nucleotide exchange factors: regulators of Rho GTPase activity in development and disease DR Cook1, KL Rossman2,3 and CJ Der1,2,3 The aberrant activity of Ras homologous (Rho) family small GTPases (20 human members) has been implicated in cancer and other human diseases. However, in contrast to the direct mutational activation of Ras found in cancer and developmental disorders, Rho GTPases are activated most commonly in disease by indirect mechanisms. One prevalent mechanism involves aberrant Rho activation via the deregulated expression and/or activity of Rho family guanine nucleotide exchange factors (RhoGEFs). RhoGEFs promote formation of the active GTP-bound state of Rho GTPases. The largest family of RhoGEFs is comprised of the Dbl family RhoGEFs with 70 human members. The multitude of RhoGEFs that activate a single Rho GTPase reflects the very specific role of each RhoGEF in controlling distinct signaling mechanisms involved in Rho activation. In this review, we summarize the role of Dbl RhoGEFs in development and disease, with a focus on Ect2 (epithelial cell transforming squence 2), Tiam1 (T-cell lymphoma invasion and metastasis 1), Vav and P-Rex1/2 (PtdIns(3,4,5)P3 (phosphatidylinositol (3,4,5)-triphosphate)-dependent Rac exchanger). Oncogene (2014) 33, 4021–4035; doi:10.1038/onc.2013.362; published online 16 September 2013 Keywords: Rac1; RhoA; Cdc42; guanine nucleotide exchange factors; cancer; -
Molecular Signatures Differentiate Immune States in Type 1 Diabetes Families
Page 1 of 65 Diabetes Molecular signatures differentiate immune states in Type 1 diabetes families Yi-Guang Chen1, Susanne M. Cabrera1, Shuang Jia1, Mary L. Kaldunski1, Joanna Kramer1, Sami Cheong2, Rhonda Geoffrey1, Mark F. Roethle1, Jeffrey E. Woodliff3, Carla J. Greenbaum4, Xujing Wang5, and Martin J. Hessner1 1The Max McGee National Research Center for Juvenile Diabetes, Children's Research Institute of Children's Hospital of Wisconsin, and Department of Pediatrics at the Medical College of Wisconsin Milwaukee, WI 53226, USA. 2The Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA. 3Flow Cytometry & Cell Separation Facility, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA. 4Diabetes Research Program, Benaroya Research Institute, Seattle, WA, 98101, USA. 5Systems Biology Center, the National Heart, Lung, and Blood Institute, the National Institutes of Health, Bethesda, MD 20824, USA. Corresponding author: Martin J. Hessner, Ph.D., The Department of Pediatrics, The Medical College of Wisconsin, Milwaukee, WI 53226, USA Tel: 011-1-414-955-4496; Fax: 011-1-414-955-6663; E-mail: [email protected]. Running title: Innate Inflammation in T1D Families Word count: 3999 Number of Tables: 1 Number of Figures: 7 1 For Peer Review Only Diabetes Publish Ahead of Print, published online April 23, 2014 Diabetes Page 2 of 65 ABSTRACT Mechanisms associated with Type 1 diabetes (T1D) development remain incompletely defined. Employing a sensitive array-based bioassay where patient plasma is used to induce transcriptional responses in healthy leukocytes, we previously reported disease-specific, partially IL-1 dependent, signatures associated with pre and recent onset (RO) T1D relative to unrelated healthy controls (uHC). -
1 Novel Expression Signatures Identified by Transcriptional Analysis
ARD Online First, published on October 7, 2009 as 10.1136/ard.2009.108043 Ann Rheum Dis: first published as 10.1136/ard.2009.108043 on 7 October 2009. Downloaded from Novel expression signatures identified by transcriptional analysis of separated leukocyte subsets in SLE and vasculitis 1Paul A Lyons, 1Eoin F McKinney, 1Tim F Rayner, 1Alexander Hatton, 1Hayley B Woffendin, 1Maria Koukoulaki, 2Thomas C Freeman, 1David RW Jayne, 1Afzal N Chaudhry, and 1Kenneth GC Smith. 1Cambridge Institute for Medical Research and Department of Medicine, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0XY, UK 2Roslin Institute, University of Edinburgh, Roslin, Midlothian, EH25 9PS, UK Correspondence should be addressed to Dr Paul Lyons or Prof Kenneth Smith, Department of Medicine, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Hills Road, Cambridge, CB2 0XY, UK. Telephone: +44 1223 762642, Fax: +44 1223 762640, E-mail: [email protected] or [email protected] Key words: Gene expression, autoimmune disease, SLE, vasculitis Word count: 2,906 The Corresponding Author has the right to grant on behalf of all authors and does grant on behalf of all authors, an exclusive licence (or non-exclusive for government employees) on a worldwide basis to the BMJ Publishing Group Ltd and its Licensees to permit this article (if accepted) to be published in Annals of the Rheumatic Diseases and any other BMJPGL products to exploit all subsidiary rights, as set out in their licence (http://ard.bmj.com/ifora/licence.pdf). http://ard.bmj.com/ on September 29, 2021 by guest. Protected copyright. 1 Copyright Article author (or their employer) 2009. -
SUPPORTING INFORMATION for Regulation of Gene Expression By
SUPPORTING INFORMATION for Regulation of gene expression by the BLM helicase correlates with the presence of G4 motifs Giang Huong Nguyen1,2, Weiliang Tang3, Ana I. Robles1, Richard P. Beyer4, Lucas T. Gray5, Judith A. Welsh1, Aaron J. Schetter1, Kensuke Kumamoto1,6, Xin Wei Wang1, Ian D. Hickson2,7, Nancy Maizels5, 3,8 1 Raymond J. Monnat, Jr. and Curtis C. Harris 1Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, U.S.A; 2Department of Medical Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, U.K.; 3Department of Pathology, University of Washington, Seattle, WA U.S.A.; 4 Center for Ecogenetics and Environmental Health, University of Washington, Seattle, WA U.S.A.; 5Department of Immunology and Department of Biochemistry, University of Washington, Seattle, WA U.S.A.; 6Department of Organ Regulatory Surgery, Fukushima Medical University, Fukushima, Japan; 7Cellular and Molecular Medicine, Nordea Center for Healthy Aging, University of Copenhagen, Denmark; 8Department of Genome Sciences, University of WA, Seattle, WA U.S.A. SI Index: Supporting Information for this manuscript includes the following 19 items. A more detailed Materials and Methods section is followed by 18 Tables and Figures in order of their appearance in the manuscript text: 1) SI Materials and Methods 2) Figure S1. Study design and experimental workflow. 3) Figure S2. Immunoblot verification of BLM depletion from human fibroblasts. 4) Figure S3. PCA of mRNA and miRNA expression in BLM-depleted human fibroblasts. 5) Figure S4. qPCR confirmation of mRNA array data. 6) Table S1. BS patient and control detail. -
ADX609 3301 Athena Newborndx Gene Panel Update 3-30-20.Indd
NewbornDx™ Advanced Sequencing Evaluation When time to diagnosis matters, the NewbornDx™ Advanced Sequencing Evaluation from Athena Diagnostics delivers rapid, 3- to 7-day results on a targeted 1,722-genes. A2ML1 ALAD ATM CAV1 CLDN19 CTNS DOCK7 ETFB FOXC2 GLUL HOXC13 JAK3 AAAS ALAS2 ATP1A2 CBL CLIC2 CTRC DOCK8 ETFDH FOXE1 GLYCTK HOXD13 JUP AARS2 ALDH18A1 ATP1A3 CBS CLMP CTSA DOK7 ETHE1 FOXE3 GM2A HPD KANK1 AASS ALDH1A2 ATP2B3 CC2D2A CLN3 CTSD DOLK EVC FOXF1 GMPPA HPGD K ANSL1 ABAT ALDH3A2 ATP5A1 CCDC103 CLN5 CTSK DPAGT1 EVC2 FOXG1 GMPPB HPRT1 KAT6B ABCA12 ALDH4A1 ATP5E CCDC114 CLN6 CUBN DPM1 EXOC4 FOXH1 GNA11 HPSE2 KCNA2 ABCA3 ALDH5A1 ATP6AP2 CCDC151 CLN8 CUL4B DPM2 EXOSC3 FOXI1 GNAI3 HRAS KCNB1 ABCA4 ALDH7A1 ATP6V0A2 CCDC22 CLP1 CUL7 DPM3 EXPH5 FOXL2 GNAO1 HSD17B10 KCND2 ABCB11 ALDOA ATP6V1B1 CCDC39 CLPB CXCR4 DPP6 EYA1 FOXP1 GNAS HSD17B4 KCNE1 ABCB4 ALDOB ATP7A CCDC40 CLPP CYB5R3 DPYD EZH2 FOXP2 GNE HSD3B2 KCNE2 ABCB6 ALG1 ATP8A2 CCDC65 CNNM2 CYC1 DPYS F10 FOXP3 GNMT HSD3B7 KCNH2 ABCB7 ALG11 ATP8B1 CCDC78 CNTN1 CYP11B1 DRC1 F11 FOXRED1 GNPAT HSPD1 KCNH5 ABCC2 ALG12 ATPAF2 CCDC8 CNTNAP1 CYP11B2 DSC2 F13A1 FRAS1 GNPTAB HSPG2 KCNJ10 ABCC8 ALG13 ATR CCDC88C CNTNAP2 CYP17A1 DSG1 F13B FREM1 GNPTG HUWE1 KCNJ11 ABCC9 ALG14 ATRX CCND2 COA5 CYP1B1 DSP F2 FREM2 GNS HYDIN KCNJ13 ABCD3 ALG2 AUH CCNO COG1 CYP24A1 DST F5 FRMD7 GORAB HYLS1 KCNJ2 ABCD4 ALG3 B3GALNT2 CCS COG4 CYP26C1 DSTYK F7 FTCD GP1BA IBA57 KCNJ5 ABHD5 ALG6 B3GAT3 CCT5 COG5 CYP27A1 DTNA F8 FTO GP1BB ICK KCNJ8 ACAD8 ALG8 B3GLCT CD151 COG6 CYP27B1 DUOX2 F9 FUCA1 GP6 ICOS KCNK3 ACAD9 ALG9 -
Transcriptome Profiling Reveals the Complexity of Pirfenidone Effects in IPF
ERJ Express. Published on August 30, 2018 as doi: 10.1183/13993003.00564-2018 Early View Original article Transcriptome profiling reveals the complexity of pirfenidone effects in IPF Grazyna Kwapiszewska, Anna Gungl, Jochen Wilhelm, Leigh M. Marsh, Helene Thekkekara Puthenparampil, Katharina Sinn, Miroslava Didiasova, Walter Klepetko, Djuro Kosanovic, Ralph T. Schermuly, Lukasz Wujak, Benjamin Weiss, Liliana Schaefer, Marc Schneider, Michael Kreuter, Andrea Olschewski, Werner Seeger, Horst Olschewski, Malgorzata Wygrecka Please cite this article as: Kwapiszewska G, Gungl A, Wilhelm J, et al. Transcriptome profiling reveals the complexity of pirfenidone effects in IPF. Eur Respir J 2018; in press (https://doi.org/10.1183/13993003.00564-2018). This manuscript has recently been accepted for publication in the European Respiratory Journal. It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Copyright ©ERS 2018 Copyright 2018 by the European Respiratory Society. Transcriptome profiling reveals the complexity of pirfenidone effects in IPF Grazyna Kwapiszewska1,2, Anna Gungl2, Jochen Wilhelm3†, Leigh M. Marsh1, Helene Thekkekara Puthenparampil1, Katharina Sinn4, Miroslava Didiasova5, Walter Klepetko4, Djuro Kosanovic3, Ralph T. Schermuly3†, Lukasz Wujak5, Benjamin Weiss6, Liliana Schaefer7, Marc Schneider8†, Michael Kreuter8†, Andrea Olschewski1, -
V1 AARS AARS AARS AARS2 ABCC9 AARS2 ABCB7 ABHD5 ABCD1
BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) J Med Genet Supplementary Table 1: Genes included on each iteration of the PathWest gene panel v1 v2 v3 neuro v3 muscle AARS AARS AARS AARS2 ABCC9 AARS2 ABCB7 ABHD5 ABCD1 ABCD1 ABCD1 ACAD9 ABHD12 ABHD12 ABHD12 ACADVL ABHD5 ABHD5 ACTB ACTA1 ACADVL ACAD9 ACTG1 ACTC1 ACADVL ACADVL ADAR ACTN2 ACTA1 ACTA1 ADCK3 ADCY6 ACTC1 ACTB ADGRG1 ADGRG6 ACTN2 ADCK3 AFG3L2 ADSSL1 ACVR1 ADCY6 AIFM1 AGK ADCK3 AFG3L2 AIMP1 AGL AFG3L2 AGK AKT1 AGRN AGL AGL AKT3 AIFM1 AGRN AGRN ALDH18A1 ALDOA AHNAK AIFM1 ALDH3A2 ALG14 AIFM1 AIMP1 ALS2 ALG2 ALDH3A2 ALDH3A2 AMPD2 AMPD1 ALS2 ALG14 ANG ANKRD1 ANG ALG2 ANO10 ANKRD2 ANK2 ALS2 ANO3 ANO5 ANKRD1 AMPD1 AP4B1 APOD ANO10 AMPD2 AP4E1 ASCC1 ANO5 ANG AP4M1 ATP1A2 AP5Z1 ANO10 AP4S1 ATP2A1 APOA1 ANO3 AP5Z1 ATP5A1 APTX ANO5 APTX B3GALNT2 AR AP4B1 ARFGEF2 B3GALT6 ARHGEF10 AP4E1 ARHGEF10 B4GAT1 ARSA AP4M1 ARL6IP1 BAG3 ARX AP4S1 ARSA BIN1 ASAH1 AP5Z1 ARSI BVES ATL1 APTX ARX C10orf2 ATM ARHGEF10 ASAH1 C12orf65 ATP2A1 ARL6IP1 ASCC1 C8orf22 ATP2B3 ARSA ASPA CA3 ATP7A ARSI ASPM CACNA1S B3GALNT2 ASAH1 ATCAY CAPN3 BAG3 ASPA ATL1 CASQ1 BEAN1 ATL1 ATL3 CAV3 BIN1 ATL3 ATM CCDC78 BSCL2 ATM ATP1A3 CD99 C10orf2 ATP1A3 ATP2B3 CEP89 CACNA1A ATP2A1 ATP2B4 CFL2 CACNA1C ATP2B3 ATP6AP2 CHAT CACNA1S ATP2B4 ATP7A CHCHD10 CACNB2 ATP5A1 ATR CHD7 CACNB4 ATP6AP2 B3GALNT2 CHKA CAPN3 ATP7A B4GALNT1 CHKB Ravenscroft G, et al. J Med Genet 2020;0:1–10. doi: -
Supplemental Data
Supplementary Table 1. Gene sets from Figure 6. Lists of genes from each individual gene set defined in Figure 6, including the fold-change in expression of each gene in treatment group pair-wise comparisons. ENSEMBL: Ensembl gene identifier; Symbol: official gene symbol; logFC: log fold change; p value: significance of fold-change in a pair-wise comparison, P<0.05 cut-off; FDR: false discovery rate, expected proportion of false positives among the differentially expressed genes in a pair-wise comparison (FDR<0.25 cut-off). Sup. Table 1 SET I CP versus Sal CP versus CP+DCA DCA versus Sal ENSEMBL Symbol logFC PValue FDR logFC PValue FDR logFC PValue FDR Desc ENSMUSG00000020326 Ccng1 2.64 0.00 0.00 -0.06 0.13 0.96 0.40 0.00 0.23 cyclin G1 [Source:MGI Symbol;Acc:MGI:102890] ENSMUSG00000031886 Ces2e 3.97 0.00 0.00 -0.24 0.02 0.28 0.01 1.00 1.00 carboxylesterase 2E [Source:MGI Symbol;Acc:MGI:2443170] ENSMUSG00000041959 S100a10 2.31 0.00 0.00 -0.21 0.02 0.23 -0.11 0.53 1.00 S100 calcium binding protein A10 (calpactin) [Source:MGI Symbol;Acc:MGI:1339468] ENSMUSG00000092341 Malat1 1.09 0.00 0.00 -0.11 0.20 1.00 0.66 0.00 0.00 metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) [Source:MGI Symbol;Acc:MGI:1919539] ENSMUSG00000072949 Acot1 1.73 0.00 0.00 -0.22 0.01 0.12 -0.44 0.01 1.00 acyl-CoA thioesterase 1 [Source:MGI Symbol;Acc:MGI:1349396] ENSMUSG00000064339 mt-Rnr2 1.09 0.00 0.00 -0.08 0.17 1.00 0.67 0.00 0.07 mitochondrially encoded 16S rRNA [Source:MGI Symbol;Acc:MGI:102492] ENSMUSG00000025934 Gsta3 1.86 0.00 0.00 -0.28