DOCSLIB.ORG

Affi ID Name Fold Change in Expression (Log2 Q Value of Correlation

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Affi ID Name Fold Change in Expression (Log2 Q Value of Correlation 263 predictors of sensitivity Affi ID Name Fold Change in expressionq value (log2 of correlation values) with sensitivity 1 201131_s_at cadherin 1, type 1, E-cadherin (epithelial), CDH17.307642345 1.25E-12 2 216905_s_at suppression of tumorigenicity 14 (colon carcinoma),5.766756751 ST14 2.74E-09 3 209016_s_at keratin 7, KRT7 6.086006959 6.72E-09 4 219010_at chromosome 1 open reading frame 106, C1orf1064.259668439 1.16E-08 5 235651_at Transcribed locus, --- 4.046173911 1.16E-08 6 201839_s_at tumor-associated calcium signal transducer 1, TACSTD15.799688725 2.55E-08 7 202826_at serine peptidase inhibitor, Kunitz type 1, SPINT13.938410734 2.55E-08 8 219513_s_at SH2 domain containing 3A, SH2D3A 4.10587049 3.48E-08 9 238689_at G protein-coupled receptor 110, GPR110 5.994870928 4.47E-08 10 205780_at BCL2-interacting killer (apoptosis-inducing), BIK3.895263692 5.20E-08 11 226863_at family with sequence similarity 110, member C,4.122710548 FAM110C 6.89E-08 12 219429_at fatty acid 2-hydroxylase, FA2H 4.662789707 7.39E-08 13 205709_s_at CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase)4.534230135 1, CDS11.93E-07 14 225301_s_at myosin VB, MYO5B 3.889534521 3.36E-07 15 226185_at CDNA: FLJ23044 fis, clone LNG02454, --- 4.08488682 3.65E-07 16 225846_at RNA binding motif protein 35A, RBM35A 6.369601269 4.06E-07 17 206482_at PTK6 protein tyrosine kinase 6, PTK6 3.836645344 4.06E-07 18 202005_at suppression of tumorigenicity 14 (colon carcinoma),3.554840755 ST14 4.06E-07 19 203287_at ladinin 1, LAD1 2.795428053 4.15E-07 20 224650_at mal, T-cell differentiation protein 2, MAL2 8.011516447 4.86E-07 21 227948_at FYVE, RhoGEF and PH domain containing 4, FGD43.009289468 4.86E-07 22 216641_s_at ladinin 1, LAD1 2.863050549 8.16E-07 23 201428_at claudin 4, CLDN4 3.289121596 9.36E-07 24 202890_at microtubule-associated protein 7, MAP7 4.330255376 1.03E-06 25 228450_at pleckstrin homology domain containing, family A3.36730706 member 7, PLEKHA71.08E-06 26 226482_s_at KAT protein /// hypothetical protein LOC100134860,3.812833583 hCG_20857 /// RP11-544M22.41.08E-06 27 229498_at Transcribed locus, --- 3.3083474 2.27E-06 28 228865_at chromosome 1 open reading frame 116, C1orf1164.141060355 2.54E-06 29 222496_s_at RNA binding motif protein 47, RBM47 3.802339025 2.60E-06 30 219395_at RNA binding motif protein 35B, RBM35B 2.86934262 2.60E-06 31 212242_at tubulin, alpha 4a, TUBA4A 2.723949809 3.34E-06 32 219856_at chromosome 1 open reading frame 116, C1orf1163.026721124 3.53E-06 33 205016_at transforming growth factor, alpha, TGFA 4.868041002 3.79E-06 34 202454_s_at v-erb-b2 erythroblastic leukemia viral oncogene4.011489315 homolog 3 (avian), ERBB33.79E-06 35 219121_s_at RNA binding motif protein 35A, RBM35A 5.213337795 4.39E-06 36 210059_s_at mitogen-activated protein kinase 13, MAPK13 3.439403362 4.85E-06 37 203780_at myelin protein zero-like 2, MPZL2 5.43068165 5.71E-06 38 201650_at keratin 19, KRT19 5.010409788 6.32E-06 39 212338_at myosin ID, MYO1D 4.061624293 6.72E-06 40 226213_at v-erb-b2 erythroblastic leukemia viral oncogene4.402713666 homolog 3 (avian), ERBB37.33E-06 41 226187_at CDNA: FLJ23044 fis, clone LNG02454, --- 2.272163205 7.33E-06 42 221664_s_at F11 receptor, F11R 2.903811195 8.46E-06 43 226129_at family with sequence similarity 83, member H,2.234354481 FAM83H 8.62E-06 44 218035_s_at RNA binding motif protein 47, RBM47 4.026439536 9.28E-06 45 202790_at claudin 7, CLDN7 3.723941513 9.28E-06 46 202889_x_at microtubule-associated protein 7, MAP7 2.448880098 9.28E-06 47 226535_at integrin, beta 6, ITGB6 5.066078964 1.09E-05 48 203397_s_at UDP-N-acetyl-alpha-D-galactosamine:polypeptide6.57082688 N-acetylgalactosaminyltransferase1.28E-05 3 (GalNAc-T3), GALNT3 49 224097_s_at F11 receptor, F11R 2.515317808 1.38E-05 50 227747_at myelin protein zero-like 3, MPZL3 2.774109051 1.67E-05 51 227224_at Ral GEF with PH domain and SH3 binding motif2.416546848 2, RALGPS2 1.67E-05 52 201130_s_at cadherin 1, type 1, E-cadherin (epithelial), CDH13.03210704 1.81E-05 53 212611_at deltex 4 homolog (Drosophila), DTX4 3.309887742 2.03E-05 54 205455_at macrophage stimulating 1 receptor (c-met-related2.035759784 tyrosine kinase), MST1R2.05E-05 55 203726_s_at laminin, alpha 3, LAMA3 4.697907932 2.12E-05 56 215471_s_at microtubule-associated protein 7, MAP7 2.168534128 2.16E-05 57 204855_at serpin peptidase inhibitor, clade B (ovalbumin),5.269561963 member 5, SERPINB52.25E-05 58 207169_x_at discoidin domain receptor tyrosine kinase 1, DDR12.433338969 2.28E-05 59 1555829_at family with sequence similarity 62 (C2 domain 2.713616271containing) member B,2.70E-05 FAM62B 60 232158_x_at NIPA-like domain containing 1, NPAL1 2.331691699 2.70E-05 61 229105_at G protein-coupled receptor 39, GPR39 2.324070942 2.86E-05 62 219476_at chromosome 1 open reading frame 116, C1orf1164.326069154 2.94E-05 63 235988_at G protein-coupled receptor 110, GPR110 4.219012291 3.53E-05 64 223000_s_at F11 receptor, F11R 3.23247497 3.53E-05 65 208779_x_at discoidin domain receptor tyrosine kinase 1, DDR12.306393546 3.87E-05 66 213285_at transmembrane protein 30B, TMEM30B 5.451573714 4.27E-05 67 210749_x_at discoidin domain receptor tyrosine kinase 1, DDR12.195281319 4.27E-05 68 212925_at chromosome 19 open reading frame 21, C19orf212.051165995 4.36E-05 69 209270_at laminin, beta 3, LAMB3 3.414304744 4.37E-05 70 210827_s_at E74-like factor 3 (ets domain transcription factor,2.814056284 epithelial-specific ), 4.66E-05ELF3 71 236279_at Transcribed locus, --- 2.3473006 5.33E-05 72 1553132_a_at tandem C2 domains, nuclear, TC2N 4.017882549 5.44E-05 73 225792_at hook homolog 1 (Drosophila), HOOK1 4.028133542 6.01E-05 74 207517_at laminin, gamma 2, LAMC2 3.704848975 6.35E-05 75 205466_s_at heparan sulfate (glucosamine) 3-O-sulfotransferase5.436458134 1, HS3ST1 7.10E-05 76 202267_at laminin, gamma 2, LAMC2 3.659775364 7.10E-05 77 226302_at ATPase, class I, type 8B, member 1, ATP8B1 3.559944948 7.10E-05 78 229139_at junctophilin 1, JPH1 2.864543075 7.10E-05 79 210058_at mitogen-activated protein kinase 13, MAPK13 2.828316235 7.10E-05 80 203556_at zinc fingers and homeoboxes 2, ZHX2 2.194538217 7.10E-05 81 218309_at calcium/calmodulin-dependent protein kinase 3.606321142II inhibitor 1, CAMK2N17.32E-05 82 208083_s_at integrin, beta 6, ITGB6 3.712019495 9.78E-05 83 219411_at engulfment and cell motility 3, ELMO3 2.199650875 0.000100662 84 242417_at hypothetical protein LOC283278, LOC283278 2.139768476 0.000107967 85 208190_s_at lipolysis stimulated lipoprotein receptor, LSR 3.14569944 0.000116241 86 226961_at proline rich 15, PRR15 3.140534919 0.000128046 87 204363_at coagulation factor III (thromboplastin, tissue factor),4.543913428 F3 0.00013936 88 225612_s_at UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase2.520816704 5,0.000141368 B3GNT5 89 235144_at CDNA FLJ32320 fis, clone PROST2003537, --- 3.459172125 0.000159857 90 239148_at MARVEL domain containing 3, MARVELD3 2.490464259 0.000159857 91 203786_s_at tumor protein D52-like 1, TPD52L1 2.659149499 0.000162177 92 211778_s_at ovo-like 2 (Drosophila), OVOL2 2.034413241 0.000164671 93 236489_at Transcribed locus, --- 4.198690925 0.000182203 94 210372_s_at tumor protein D52-like 1, TPD52L1 2.984241897 0.000182203 95 218186_at RAB25, member RAS oncogene family, RAB25 4.900922875 0.000194054 96 205538_at coronin, actin binding protein, 2A, CORO2A 2.141455538 0.000197861 97 204679_at potassium channel, subfamily K, member 1, KCNK13.44169771 0.000198351 98 1554246_at chromosome 1 open reading frame 210, C1orf2102.042255551 0.00021331 99 202546_at vesicle-associated membrane protein 8 (endobrevin),2.635457349 VAMP8 0.000215004 100 204678_s_at potassium channel, subfamily K, member 1, KCNK13.260516811 0.000216703 101 226707_at nicotinate phosphoribosyltransferase domain containing2.152294272 1, NAPRT10.000224696 102 217551_at similar to olfactory receptor, family 7, subfamily3.099141657 A, member 17, LOC4414530.000231699 103 235148_at keratinocyte associated protein 3, KRTCAP3 2.720121851 0.00024997 104 232112_at Ral GEF with PH domain and SH3 binding motif2.022332645 2, RALGPS2 0.000254329 105 238805_at chromosome 11 open reading frame 52, C11orf522.020320891 0.000254329 106 238028_at hypothetical protein LOC100128918, LOC1001289182.012735509 0.000254329 107 218885_s_at UDP-N-acetyl-alpha-D-galactosamine:polypeptide3.360938063 N-acetylgalactosaminyltransferase0.000260386 12 (GalNAc-T12), GALNT12 108 235141_at MARVEL domain containing 2, MARVELD2 2.114799736 0.000260386 109 220468_at ADP-ribosylation factor-like 14, ARL14 4.513249745 0.000280029 110 201015_s_at junction plakoglobin, JUP 2.966542201 0.000280029 111 207717_s_at plakophilin 2, PKP2 3.178773866 0.000281622 112 1565162_s_at microsomal glutathione S-transferase 1, MGST13.070520945 0.000293166 113 219936_s_at G protein-coupled receptor 87, GPR87 4.347615139 0.000320229 114 209369_at annexin A3, ANXA3 4.826236725 0.000336537 115 238673_at Sterile alpha motif domain containing 12, SAMD123.481911155 0.000352147 116 218804_at transmembrane protein 16A, TMEM16A 4.459670582 0.000377042 117 231311_at CDNA FLJ11417 fis, clone HEMBA1000960, --- 2.00750352 0.000390181 118 235924_at CDNA FLJ42287 fis, clone TLIVE2005866, --- 2.910860666 0.000392716 119 202286_s_at tumor-associated calcium signal transducer 2, TACSTD25.885434234 0.000406216 120 212531_at lipocalin 2, LCN2 4.255205979 0.000406216 121 224918_x_at microsomal glutathione S-transferase 1, MGST12.680501799 0.000406216 122 214581_x_at tumor necrosis factor receptor superfamily, member2.842936317 21, TNFRSF210.000408639 123 227177_at
Load more

Recommended publications
  • Molecular Biology and Biochemistry of The
    MOLECULAR BIOLOGY AND BIOCHEMISTRY OF THE REGULATION OF HRP/TYPE III SECRETION GENES IN THE CORN PATHOGEN PANTOEA STEWARTII SUBSP. STEWARTII DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Massimo Merighi, B. S., M. S. ***** The Ohio State University 2003 Dissertation Committee: Professor David L. Coplin, Adviser Approved by Professor Brian Ahmer ______________________ Professor Dietz W. Bauer Adviser Professor Terrence L. Graham Plant Pathology Copyright by Massimo Merighi 2003 ii ABSTRACT Pantoea stewartii subsp. stewartii is a bacterial pathogen of corn. Its pathogenicity depends on the expression of a Hrp/type III protein secretion/translocation system. The regulatory region of the hrp gene cluster consists of three adjacent operons: hrpXY encodes a two- component regulatory system, consisting of the response regulator HrpY and sensor PAS-kinase HrpX; hrpS encodes an NtrC-like enhancer-binding protein; and hrpL encodes an ECF sigma factor. In this study, we used genetic and biochemical approaches to delineate the following regulatory cascade: 1) HrpY activates hrpS; 2) HrpS activates hrpL; and 3) HrpL activates secretion and effector genes with ‘Hrp-box’ promoters. This pathway responds to environmental signals and global regulators. Mutant analysis showed that HrpX is required for full virulence. Deletion of its individual PAS-sensory domains revealed that they are not redundant and each may have a different role in modulating kinase activity. HrpX probably senses an intracellular signal, possibly related to nitrogen metabolism. pH, osmolarity and nicotinic acid controlled expression of hrpS independently of HrpX/HrpY.
    [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]
  • 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]
  • Cellular and Molecular Signatures in the Disease Tissue of Early
    Cellular and Molecular Signatures in the Disease Tissue of Early Rheumatoid Arthritis Stratify Clinical Response to csDMARD-Therapy and Predict Radiographic Progression Frances Humby1,* Myles Lewis1,* Nandhini Ramamoorthi2, Jason Hackney3, Michael Barnes1, Michele Bombardieri1, Francesca Setiadi2, Stephen Kelly1, Fabiola Bene1, Maria di Cicco1, Sudeh Riahi1, Vidalba Rocher-Ros1, Nora Ng1, Ilias Lazorou1, Rebecca E. Hands1, Desiree van der Heijde4, Robert Landewé5, Annette van der Helm-van Mil4, Alberto Cauli6, Iain B. McInnes7, Christopher D. Buckley8, Ernest Choy9, Peter Taylor10, Michael J. Townsend2 & Costantino Pitzalis1 1Centre for Experimental Medicine and Rheumatology, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK. Departments of 2Biomarker Discovery OMNI, 3Bioinformatics and Computational Biology, Genentech Research and Early Development, South San Francisco, California 94080 USA 4Department of Rheumatology, Leiden University Medical Center, The Netherlands 5Department of Clinical Immunology & Rheumatology, Amsterdam Rheumatology & Immunology Center, Amsterdam, The Netherlands 6Rheumatology Unit, Department of Medical Sciences, Policlinico of the University of Cagliari, Cagliari, Italy 7Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow G12 8TA, UK 8Rheumatology Research Group, Institute of Inflammation and Ageing (IIA), University of Birmingham, Birmingham B15 2WB, UK 9Institute of
    [Show full text]
  • Application of Hidden Markov Model Based Methods for Gaining Insights Into Protein Domain Evolution and Function
    University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2015 Application of Hidden Markov Model based methods for gaining insights into protein domain evolution and function Amit Anil Upadhyay University of Tennessee - Knoxville, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Part of the Bioinformatics Commons, Computational Biology Commons, and the Genomics Commons Recommended Citation Upadhyay, Amit Anil, "Application of Hidden Markov Model based methods for gaining insights into protein domain evolution and function. " PhD diss., University of Tennessee, 2015. https://trace.tennessee.edu/utk_graddiss/3557 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Amit Anil Upadhyay entitled "Application of Hidden Markov Model based methods for gaining insights into protein domain evolution and function." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Life Sciences. Igor B. Jouline, Major Professor We have
    [Show full text]
  • Tianhua Feng
    A Comprehensive Dynamical Model for Human CaV1.2 Ion Channel: Structural and Functional Studies by Tianhua Feng A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Pharmaceutical Sciences Faculty of Pharmacy and Pharmaceutical Sciences University of Alberta © Tianhua Feng, 2019 Tianhua Feng M.Sc. Thesis SEP 2019 ABSTRACT Human CaV1.2 is a voltage-gated calcium channel (VGCC), which plays an essential role to maintain a normal cardiac function. Any abnormalities in CaV1.2 can lead to serious cardiac diseases (e.g. cardiac arrhythmias and Timothy syndrome). Thus, understanding the structure- function-dynamics relationships of CaV1.2 is important to avoid and develop treatments of these diseases. Several small molecules (e.g. dihydropyridines and phenylalkylamine) have been identified and designed to modulate the activity of CaV1.2. Yet, their mode and site of action within the CaV1.2 channel are still unclear. In order to understand how these drugs interact with CaV1.2, a detailed three-dimensional structure of the human CaV1.2 channel is necessary. However, such structures have not been resolved yet. Toward this goal, this thesis employed computational molecular modeling techniques to model the transmembrane 1-subunit three-dimensional (3D) structure of the open and closed CaV1.2 channel. We used a combination of homology modeling and threading approaches along with classical and advanced molecular dynamics simulations to explore the conformational transitions between the closed and the open states of the channel. The ultimate goal was to predict the binding orientation and critical interactions for known CaV1.2 modulators.
    [Show full text]
  • Research2007herschkowitzetvolume Al
    Open Access Research2007HerschkowitzetVolume al. 8, Issue 5, Article R76 Identification of conserved gene expression features between comment murine mammary carcinoma models and human breast tumors Jason I Herschkowitz¤*†, Karl Simin¤‡, Victor J Weigman§, Igor Mikaelian¶, Jerry Usary*¥, Zhiyuan Hu*¥, Karen E Rasmussen*¥, Laundette P Jones#, Shahin Assefnia#, Subhashini Chandrasekharan¥, Michael G Backlund†, Yuzhi Yin#, Andrey I Khramtsov**, Roy Bastein††, John Quackenbush††, Robert I Glazer#, Powel H Brown‡‡, Jeffrey E Green§§, Levy Kopelovich, reviews Priscilla A Furth#, Juan P Palazzo, Olufunmilayo I Olopade, Philip S Bernard††, Gary A Churchill¶, Terry Van Dyke*¥ and Charles M Perou*¥ Addresses: *Lineberger Comprehensive Cancer Center. †Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. ‡Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA. reports §Department of Biology and Program in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. ¶The Jackson Laboratory, Bar Harbor, ME 04609, USA. ¥Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. #Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA. **Department of Pathology, University of Chicago, Chicago, IL 60637, USA. ††Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA. ‡‡Baylor College of Medicine, Houston, TX 77030, USA. §§Transgenic Oncogenesis Group, Laboratory of Cancer Biology and Genetics. Chemoprevention Agent Development Research Group, National Cancer Institute, Bethesda, MD 20892, USA. Department of Pathology, Thomas Jefferson University, Philadelphia, PA 19107, USA. Section of Hematology/Oncology, Department of Medicine, Committees on Genetics and Cancer Biology, University of Chicago, Chicago, IL 60637, USA.
    [Show full text]
  • NIH Public Access Author Manuscript Dev Biol
    NIH Public Access Author Manuscript Dev Biol. Author manuscript; available in PMC 2013 January 1. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Dev Biol. 2012 January 1; 361(1): 68±78. doi:10.1016/j.ydbio.2011.10.004. Regulation of intrahepatic biliary duct morphogenesis by Claudin 15-like b Isla D. Cheung1, Michel Bagnat1,2, Taylur P. Ma3, Anirban Datta4, Kimberley Evason1,5, John C. Moore6, Nathan Lawson6, Keith E. Mostov4, Cecilia B. Moens3, and Didier Y.R. Stainier1,* 1Department of Biochemistry and Biophysics; Programs in Developmental and Stem Cell Biology, Genetics and Human Genetics; Liver Center, Diabetes Center, and Institute for Regeneration Medicine; University of California, San Francisco, CA 94158, USA 3HHMI and Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA 4Department of Anatomy, University of California, San Francisco, CA 94143, USA 5Department of Pathology, University of California, San Francisco, CA 94110, USA 6Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA 01605, USA Abstract The intrahepatic biliary ducts transport bile produced by the hepatocytes out of the liver. Defects in biliary cell differentiation and biliary duct remodeling cause a variety of congenital diseases including Alagille Syndrome and polycystic liver disease. While the molecular pathways regulating biliary cell differentiation have received increasing attention (Lemaigre, 2010), less is known about the cellular behavior underlying biliary duct remodeling. Here, we have identified a novel gene, claudin 15-like b (cldn15lb), which exhibits a unique and dynamic expression pattern in the hepatocytes and biliary epithelial cells in zebrafish.
    [Show full text]
  • Supplementary Table 1A. Genes Significantly Altered in A4573 ESFT
    Supplementary Table 1A. Genes significantly altered in A4573 ESFT cells following BMI-1knockdown genesymbol genedescription siControl siBMI1 FC Direction P-value AASS aminoadipate-semialdehyde synthase | tetra-peptide repeat homeobox-like6.68 7.24 1.5 Up 0.007 ABCA2 ATP-binding cassette, sub-family A (ABC1), member 2 | neural5.44 proliferation,6.3 differentiation1.8 and Upcontrol, 1 0.006 ABHD4 abhydrolase domain containing 4 7.51 6.69 1.8 Down 0.002 ACACA acetyl-Coenzyme A carboxylase alpha | peroxiredoxin 5 | similar6.2 to High mobility7.26 group2.1 protein UpB1 (High mobility0.009 group protein 1) (HMG-1) (Amphoterin) (Heparin-binding protein p30) | Coenzyme A synthase ACAD9 acyl-Coenzyme A dehydrogenase family, member 9 9.25 8.59 1.6 Down 0.008 ACBD3 acyl-Coenzyme A binding domain containing 3 7.89 8.53 1.6 Up 0.008 ACCN2 amiloride-sensitive cation channel 2, neuronal 5.47 6.28 1.8 Up 0.005 ACIN1 apoptotic chromatin condensation inducer 1 7.15 7.79 1.6 Up 0.008 ACPL2 acid phosphatase-like 2 6.04 7.6 2.9 Up 0.000 ACSL4 acyl-CoA synthetase long-chain family member 4 6.72 5.8 1.9 Down 0.001 ACTA2 actin, alpha 2, smooth muscle, aorta 9.18 8.44 1.7 Down 0.003 ACYP1 acylphosphatase 1, erythrocyte (common) type 7.09 7.66 1.5 Up 0.009 ADA adenosine deaminase 6.34 7.1 1.7 Up 0.009 ADAL adenosine deaminase-like 7.88 6.89 2.0 Down 0.006 ADAMTS1 ADAM metallopeptidase with thrombospondin type 1 motif, 1 6.57 7.65 2.1 Up 0.000 ADARB1 adenosine deaminase, RNA-specific, B1 (RED1 homolog rat) 6.49 7.13 1.6 Up 0.008 ADCY9 adenylate cyclase 9 6.5 7.18
    [Show full text]
  • Novel Compound Heterozygote Mutations of TJP2 in a Chinese
    Ge et al. BMC Medical Genetics (2019) 20:18 https://doi.org/10.1186/s12881-019-0753-7 CASEREPORT Open Access Novel compound heterozygote mutations of TJP2 in a Chinese child with progressive cholestatic liver disease Ting Ge, Xinyue Zhang, Yongmei Xiao, Yizhong Wang* and Ting Zhang* Abstract Background: Progressive familial intrahepatic cholestasis (PFIC) is a group of genetic autosomal recessive disorders that predominantly affects young children and results in early-onset progressive liver damage. Several types of PFIC were defined based on different genetic aetiologies in last decades. Case presentation: Here, we report a Chinese young child diagnosed as PFIC with variants in tight junction protein 2 (TJP2). The patient was affected by a long history of jaundice, pruritus, and failure to thrive. Highly elevated level of serum total bile acid (TBA) and normal levels of gamma-glutamyltransferase (GGT) were observed at hospitalization. The patient’s clinical symptoms could be alleviated by administration of ursodeoxycholic acid. Genetic testing by next generation sequencing (NGS) found novel compound heterozygote mutations c.2448 + 1G > C/c.2639delC (p.T880Sfs*12) in TJP2, which were inherited from her mother and father, respectively. Both mutations were predicted to abolish TJP2 protein translation, and neither has previously been identified. Conclusion: We report a Chinese female PFIC child with novel compound heterozygous mutations of TJP2.Genetic testing by NGS is valuable in the clinical diagnosis of hereditary liver disease. Keywords: Autosomal recessive disorder, Child, Compound heterozygote mutations, Progressive cholestatic liver disease, TJP2 Background in adenosine triphosphate-binding cassette subfamily B Progressive familial intrahepatic cholestasis (PFIC), first de- member 4 (ABCB4), which encodes the multidrug scribed in 1969, is a group of genetic autosomal recessive resistance P-glycoprotein 3 protein (MDR3) leads to disorders that are characterized by fluctuating jaundice, the development of PFIC 3 [5].
    [Show full text]
  • A Novel Homozygous USP53 Splicing Variant Disrupting the Gene Function That Causes Cholestasis Phenotype and Review of the Literature
    A Novel Homozygous USP53 Splicing Variant Disrupting the Gene Function that Causes Cholestasis Phenotype and Review of the Literature ALPER GEZDIRICI ( [email protected] ) Basaksehir Cam and Sakura City Hospital https://orcid.org/0000-0002-2432-9279 ÖZLEM KALAYCIK ŞENGÜL İstanbul Kanuni Sultan Süleyman Eğitim ve Araştırma Hastanesi: Istanbul Kanuni Sultan Suleyman Egitim ve Arastirma Hastanesi MUSTAFA DOĞAN Basaksehir Cam and Sakura City Hospital BANU YILMAZ ÖZGÜVEN Basaksehir Cam and Sakura City Hospital EKREM AKBULUT Malatya Turgut Özal Üniversitesi: Malatya Turgut Ozal Universitesi Research Article Keywords: USP53, cholestasis, homology modeling, whole exome sequencing Posted Date: August 12th, 2021 DOI: https://doi.org/10.21203/rs.3.rs-762230/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/19 Abstract Background: Hereditary cholestasis is a heterogeneous group of liver diseases that mostly show autosomal recessive inheritance. The phenotype of cholestasis is highly variable. Molecular genetic testing offers a useful approach to differentiate different types of cholestasis because some symptoms and ndings overlap. Biallelic variants in USP53 have recently been reported in cholestasis phenotype. In this study we aim to characterize clinical ndings and biological insights on a novel USP53 splice variant causing cholestasis phenotype and review of the literature. Methods and Results: We reported a novel splice variant (NM_019050.2:c.238-1G>C) in the USP53 gene via whole exome sequencing in a patient with cholestasis phenotype. This variant was conrmed by sanger sequencing and as a result of family segregation analysis; it was found to be a heterozygous state in the parents and the other healthy elder brother of our patient.
    [Show full text]
  • Protective Effects of Propionate Upon the Blood–Brain Barrier
    bioRxiv preprint doi: https://doi.org/10.1101/170548; this version posted February 7, 2018. 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-NC-ND 4.0 International license. 1 Microbiome–host systems interactions: Protective effects of propionate upon 2 the blood–brain barrier 3 4 Lesley Hoyles1*, Tom Snelling1, Umm-Kulthum Umlai1, Jeremy K. Nicholson1, Simon 5 R. Carding2, 3, Robert C. Glen1, 4 & Simon McArthur5* 6 7 1Division of Integrative Systems Medicine and Digestive Disease, Department of 8 Surgery and Cancer, Imperial College London, UK 9 2Norwich Medical School, University of East Anglia, UK 10 3The Gut Health and Food Safety Research Programme, The Quadram Institute, 11 Norwich Research Park, Norwich, UK 12 4Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, 13 Cambridge, UK 14 5Institute of Dentistry, Barts & the London School of Medicine & Dentistry, Blizard 15 Institute, Queen Mary University of London, London, UK 16 17 *Corresponding authors: Lesley Hoyles, [email protected]; Simon 18 McArthur, [email protected] 19 Running title: Propionate affects the blood–brain barrier 20 Abbreviations: ADHD, attention-deficit hyperactivity disorder; ASD, autism spectrum 21 disorder; BBB, blood–brain barrier; CNS, central nervous system; FFAR, free fatty acid 22 receptor; KEGG, Kyoto Encyclopaedia of Genes and Genomes; GO, Gene Ontology; 1 bioRxiv preprint doi: https://doi.org/10.1101/170548; this version posted February 7, 2018. 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]