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Supplemental Table 1 List of Genes Differentially Expressed In

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Supplemental Table 1 List of genes differentially expressed in normal nasopharyngeal epithelium (N), metaplastic and displastic lesions (R), and carcinoma (T). Parametric Permutation Geom Geom Geom Unique Description Clone UG Gene symbol Map p-value p-value mean mean mean id cluster of of of ratios ratios ratios in in in class class class 1 : N 2 : R 3 : T 1 p < 1e-07 0 0.061 0.123 2.708 169329 secretory leukocyte protease IncytePD:2510171 Hs.251754 SLPI 20q12 inhibitor (antileukoproteinase) 2 p < 1e-07 0 0.125 0.394 1.863 163628 sodium channel, nonvoltage-gated IncytePD:1453049 Hs.446415 SCNN1A 12p13 1 alpha 3 p < 1e-07 0 0.122 0.046 1.497 160401 carcinoembryonic antigen-related IncytePD:2060355 Hs.73848 CEACAM6 19q13.2 cell adhesion molecule 6 (non- specific cross reacting antigen) 4 p < 1e-07 0 0.675 1.64 5.594 165101 monoglyceride lipase IncytePD:2174920 Hs.6721 MGLL 3q21.3 5 p < 1e-07 0 0.182 0.487 0.998 166827 nei endonuclease VIII-like 1 (E. IncytePD:1926409 Hs.28355 NEIL1 15q22.33 coli) 6 p < 1e-07 0 0.194 0.339 0.915 162931 hypothetical protein FLJ22418 IncytePD:2816379 Hs.36563 FLJ22418 1p11.1 7 p < 1e-07 0 1.313 0.645 13.593 162399 S100 calcium binding protein P IncytePD:2060823 Hs.2962 S100P 4p16 8 p < 1e-07 0 0.157 1.445 2.563 169315 selenium binding protein 1 IncytePD:2591494 Hs.334841 SELENBP1 1q21-q22 9 p < 1e-07 0 0.046 0.738 1.213 160115 prominin-like 1 (mouse) IncytePD:2070568 Hs.112360 PROML1 4p15.33 10 p < 1e-07 0 0.787 2.264 3.013 167294 HRAS-like suppressor 3 IncytePD:1969263 Hs.37189 HRASLS3 11q12.3 11 p < 1e-07 0 0.292 0.539 1.493 168221 Homo sapiens cDNA FLJ13510 IncytePD:64451 Hs.37896 2 fis, clone PLACE1005146. 12 p < 1e-07 0 1.816 4.162 5.231 159872 emerin (Emery-Dreifuss muscular IncytePD:1901168 Hs.2985 EMD Xq28 dystrophy) 13 p < 1e-07 0 0.096 0.237 1.251 168256 B-factor, properdin IncytePD:167371 Hs.69771 BF 6p21.3 14 p < 1e-07 0 0.112 0.566 1.205 161755 Incyte EST IncytePD:1507769 15 p < 1e-07 0 0.113 0.366 0.603 161021 zinc finger protein 204 IncytePD:1454640 Hs.8198 ZNF204 6p21.3 16 p < 1e-07 0 0.079 0.575 0.519 168604 amylase, alpha 2B; pancreatic IncytePD:254081 Hs.335493 AMY2B 1p21 17 p < 1e-07 0 0.587 1.038 0.785 168160 zinc finger protein 161 homolog IncytePD:2487368 Hs.156000 ZFP161 18pter- (mouse) p11.2 18 1e-07 0 0.376 0.972 1.84 167971 Meis1, myeloid ecotropic viral IncytePD:1662216 Hs.380923 MEIS3 17p11.2 integration site 1 homolog 3 (mouse) 19 1e-07 0 0.048 0.247 0.388 162648 retinoic acid receptor responder IncytePD:1982324 Hs.82547 RARRES1 3q25.32 (tazarotene induced) 1 20 1e-07 0 0.231 0.783 0.812 164495 hypothetical protein LOC283445 IncytePD:1968776 Hs.234898 LOC283445 12q24.12 21 1e-07 0 0.423 0.975 1.436 163838 family with sequence similarity 13, IncytePD:1458366 Hs.177664 FAM13A1 4q22.1 member A1 22 1e-07 0 0.538 0.644 1.867 166314 LIM domain only 2 (rhombotin- IncytePD:1383888 Hs.184585 LMO2 11p13 like 1) 23 1e-07 0 0.023 0.095 0.53 164946 polymeric immunoglobulin IncytePD:1800114 Hs.205126 PIGR 1q31-q41 receptor 24 1e-07 0 0.283 0.959 1.196 163419 calmin (calponin-like, IncytePD:1464613 Hs.406099 CLMN 14q32.2 transmembrane) 25 1e-07 0 0.477 1.445 1.307 162175 truncated calcium binding protein IncytePD:1943110 Hs.351621 LOC51149 5q35.3 26 1e-07 0 0.481 0.977 1.168 163378 hypothetical protein IncytePD:2921913 Hs.48219 DKFZp434M033 12q23.2 DKFZp434M0331 27 1e-07 0 0.252 0.233 1.726 166900 likely ortholog of mouse tumor IncytePD:429577 Hs.44208 FLJ23153 7q21.12 necrosis-alpha-induced adipose- related protein 28 1e-07 0 0.572 1.406 1.553 165608 REMOVED_FROM_DATABASE IncytePD:91009 29 1e-07 0 0.379 1.149 1.305 165030 galactosamine (N-acetyl)-6-sulfate IncytePD:2903239 Hs.159479 GALNS 16q24.3 sulfatase (Morquio syndrome, mucopolysaccharidosis type IVA) 30 1e-07 0 0.27 0.949 0.925 160243 iduronate 2-sulfatase (Hunter IncytePD:549290 Hs.172458 IDS Xq28 syndrome) 31 1e-07 0 0.401 0.79 1.775 168767 protein tyrosine phosphatase, IncytePD:2941607 Hs.19718 PTPRU 1p35.3- receptor type, U p35.1 32 1e-07 0 0.032 0.239 1.15 166595 microseminoprotein, beta- IncytePD:3970665 33 1e-07 0 0.653 1.184 1.978 159959 Fanconi anemia, complementation IncytePD:1647354 group A 34 1e-07 0 1.376 0.457 0.853 168559 tripartite motif-containing 16 IncytePD:1996011 Hs.241305 TRIM16 17p11.2 35 1e-07 0 0.682 1.36 1.532 162892 KIAA1228 protein IncytePD:2667106 Hs.306867 KIAA1228 7q36.3 36 2e-07 0 0.261 2.62 3.645 164879 serum amyloid A4, constitutive IncytePD:86390 Hs.1955 SAA4 11p15.1- p14 37 2e-07 0 0.67 1.763 1.345 168694 acylphosphatase 1, erythrocyte IncytePD:1995749 Hs.18573 ACYP1 14q24.3 (common) type 38 2e-07 0 0.962 2.243 2.478 162612 Rho-related BTB domain IncytePD:2095275 Hs.15099 RHOBTB1 10q21.2 containing 1 39 2e-07 0 0.097 0.26 0.515 165530 cytochrome P450, family 2, IncytePD:1597231 Hs.152096 CYP2J2 1p31.3- subfamily J, polypeptide 2 p31.2 40 2e-07 0 0.239 0.683 0.979 165148 Homo sapiens, clone IncytePD:1666815 Hs.72080 21 IMAGE:4766144, mRNA 41 2e-07 0 0.801 0.319 0.361 168279 Homo sapiens, Similar to IncytePD:1987866 Hs.106771 5 hypothetical protein B430208I01, clone IMAGE:5181522, mRNA, partial cds 42 2e-07 0 0.072 0.298 0.917 166593 Wilms tumor associated protein IncytePD:2997479 Hs.251573 WIT-1 11p13 43 2e-07 0 1.298 1.911 5.067 167270 keratin 7 IncytePD:1649959 Hs.23881 KRT7 12q12- q13 44 2e-07 0 0.074 0.428 0.661 166636 ESTs, Weakly similar to neuronal IncytePD:2714867 Hs.436950 11 thread protein [Homo sapiens] [H.sapiens] 45 3e-07 0 0.41 4.837 4.942 164490 carboxylesterase 1 IncytePD:1813269 Hs.76688 CES1 16q13- (monocyte/macrophage serine q22.1 esterase 1) 46 3e-07 0 0.643 2.729 4.235 165666 ribonuclease, RNase A family, 4 IncytePD:1858905 Hs.283749 RNASE4 14q11.1 47 3e-07 0 0.449 1.314 1.636 162294 calcium channel, voltage- IncytePD:2057662 Hs.250712 CACNB3 12q13 dependent, beta 3 subunit 48 3e-07 0 0.132 0.48 0.78 160334 ATPase, Class II, type 9A IncytePD:1942046 Hs.406434 ATP9A 20q13.11- q13.2 49 4e-07 0 0.12 0.591 1.034 161500 regulatory factor X, 2 (influences IncytePD:2674796 Hs.100007 RFX2 19p13.3- HLA class II expression) p13.2 50 4e-07 0 0.124 0.079 0.726 160357 coagulation factor III IncytePD:2061594 Hs.62192 F3 1p22-p21 (thromboplastin, tissue factor) 51 4e-07 0 0.225 0.531 0.869 160168 kinesin family member 13B IncytePD:2708596 Hs.15711 KIF13B 8p12 52 5e-07 0 0.496 0.83 0.872 160625 myeloid/lymphoid or mixed- IncytePD:1887185 Hs.114765 MLLT2 4q21 lineage leukemia (trithorax homolog, Drosophila); translocated to, 2 53 5e-07 0 0.753 1.526 1.27 162298 hypothetical protein LOC90410 IncytePD:1552481 Hs.4187 LOC90410 17q11.1 54 5e-07 0 0.112 0.193 0.311 160654 B-cell CLL/lymphoma 6 (zinc IncytePD:1569189 Hs.155024 BCL6 3q27 finger protein 51) 55 6e-07 0 0.25 0.915 1.585 159838 aldehyde dehydrogenase 3 family, IncytePD:2610218 Hs.83155 ALDH3B1 11q13 member B1 56 6e-07 0 0.104 0.771 1.25 160072 solute carrier family 22 (organic IncytePD:1308162 Hs.77239 SLC22A4 5q31.1 cation transporter), member 4 57 6e-07 0 0.092 0.417 0.466 166685 KIAA0675 gene product IncytePD:1794725 Hs.165662 KIAA0675 3q13.12 58 7e-07 0 0.295 0.505 0.693 165716 complement component 5 receptor IncytePD:1447909 Hs.2161 C5R1 19q13.3- 1 (C5a ligand) q13.4 59 7e-07 0 0.669 1.017 2.773 169559 E74-like factor 3 (ets domain IncytePD:1988412 Hs.166096 ELF3 1q32.2 transcription factor, epithelial- specific ) 60 7e-07 0 0.736 1.472 1.208 169562 CDC16 cell division cycle 16 IncytePD:1413704 Hs.1592 CDC16 13q34 homolog (S. cerevisiae) 61 8e-07 0 0.099 0.766 5.296 165371 trefoil factor 3 (intestinal) IncytePD:2242817 Hs.82961 TFF3 21q22.3 62 8e-07 0 0.587 1.254 1.723 164531 Homo sapiens cDNA: FLJ22050 IncytePD:2868216 Hs.173705 4 fis, clone HEP09454. 63 8e-07 0 0.175 0.465 0.618 163376 ESTs IncytePD:2818878 Hs.32135 20 64 8e-07 0 0.21 0.664 0.872 163828 mucin 5, subtype B, IncytePD:1737280 Hs.102482 MUC5B 11p15 tracheobronchial 65 8e-07 0 0.327 0.686 0.7 164891 paired box gene 2 IncytePD:194662 Hs.155644 PAX2 10q22.1- q24.3 66 8e-07 0 0.114 0.079 0.535 160506 UDP glycosyltransferase 1 family, IncytePD:86450 Hs.278896 UGT1A1 2q37 polypeptide A1 67 9e-07 0 0.656 1.628 1.865 168674 Homo sapiens, clone IncytePD:1964852 Hs.427683 10 IMAGE:5587702, mRNA 68 9e-07 0 0.414 0.326 1.223 166348 epidermal growth factor receptor IncytePD:1395088 Hs.28907 EPS8R1 19q13.42 pathway substrate 8-related protein 1 69 9e-07 0 0.127 0.349 0.64 166331 Arg/Abl-interacting protein IncytePD:1495766 Hs.379795 ARGBP2 4q35.1 ArgBP2 70 9e-07 0 1.011 2.238 2.34 169526 transducin-like enhancer of split 2 IncytePD:1236828 Hs.332173 TLE2 19p13.3 (E(sp1) homolog, Drosophila) 71 9e-07 0 0.103 0.574 0.967 169644 hypothetical protein MGC27085 IncytePD:1256859 Hs.120277 MGC27085 3q26.31 72 9e-07 0 0.01 0.039 0.431 161792 tetraspan 1 IncytePD:2989680 Hs.38972 TSPAN-1 1p33 73 1e-06 0 0.17 0.872 1.348 163423 Incyte EST IncytePD:2279991 74 1e-06 0 0.238 0.485 0.47 159850 Homo sapiens cDNA FLJ34315 IncytePD:1734634 Hs.376655 14 fis, clone FEBRA2008341.
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  • KLF2 Induced

    KLF2 Induced

    UvA-DARE (Digital Academic Repository) The transcription factor KLF2 in vascular biology Boon, R.A. Publication date 2008 Link to publication Citation for published version (APA): Boon, R. A. (2008). The transcription factor KLF2 in vascular biology. General rights It is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), other than for strictly personal, individual use, unless the work is under an open content license (like Creative Commons). Disclaimer/Complaints regulations If you believe that digital publication of certain material infringes any of your rights or (privacy) interests, please let the Library know, stating your reasons. In case of a legitimate complaint, the Library will make the material inaccessible and/or remove it from the website. Please Ask the Library: https://uba.uva.nl/en/contact, or a letter to: Library of the University of Amsterdam, Secretariat, Singel 425, 1012 WP Amsterdam, The Netherlands. You will be contacted as soon as possible. UvA-DARE is a service provided by the library of the University of Amsterdam (https://dare.uva.nl) Download date:23 Sep 2021 Supplementary data: Genes induced by KLF2 Dekker et al. LocusLink Accession Gene Sequence Description Fold p-value ID number symbol change (FDR) 6654 AK022099 SOS1 cDNA FLJ12037 fis, clone HEMBB1001921. 100.00 5.9E-09 56999 AF086069 ADAMTS9 full length insert cDNA clone YZ35C05. 100.00 1.2E-09 6672 AF085934 SP100 full length insert cDNA clone YR57D07. 100.00 6.7E-13 9031 AF132602 BAZ1B Williams Syndrome critical region WS25 mRNA, partial sequence.
  • A Genome-Wide Association Study Lystra P

    A Genome-Wide Association Study Lystra P

    Hayden et al. Respiratory Research (2018) 19:209 https://doi.org/10.1186/s12931-018-0890-0 RESEARCH Open Access Childhood asthma is associated with COPD and known asthma variants in COPDGene: a genome-wide association study Lystra P. Hayden1,2* , Michael H. Cho2,3, Benjamin A. Raby1,2,3, Terri H. Beaty4, Edwin K. Silverman2,3, Craig P. Hersh2,3 and on behalf of the COPDGene Investigators Abstract Background: Childhood asthma is strongly influenced by genetics and is a risk factor for reduced lung function and chronic obstructive pulmonary disease (COPD) in adults. This study investigates self-reported childhood asthma in adult smokers from the COPDGene Study. We hypothesize that childhood asthma is associated with decreased lung function, increased risk for COPD, and that a genome-wide association study (GWAS) will show association with established asthma variants. Methods: We evaluated current and former smokers ages 45–80 of non-Hispanic white (NHW) or African American (AA) race. Childhood asthma was defined by self-report of asthma, diagnosed by a medical professional, with onset at < 16 years or during childhood. Subjects with a history of childhood asthma were compared to those who never had asthma based on lung function, development of COPD, and genetic variation. GWAS was performed in NHW and AA populations, and combined in meta-analysis. Two sets of established asthma SNPs from published literature were examined for association with childhood asthma. Results: Among 10,199 adult smokers, 730 (7%) reported childhood asthma and 7493 (73%) reported no history of asthma. Childhood asthmatics had reduced lung function and increased risk for COPD (OR 3.42, 95% CI 2.81–4.18).
  • Downloaded from GEO

    Downloaded from GEO

    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.17.252007; this version posted November 3, 2020. 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 4.0 International license. Oxylipin metabolism is controlled by mitochondrial b-oxidation during bacterial inflammation. Mariya Misheva1, Konstantinos Kotzamanis1*, Luke C Davies1*, Victoria J Tyrrell1, Patricia R S Rodrigues1, Gloria A Benavides2, Christine Hinz1, Robert C Murphy3, Paul Kennedy4, Philip R Taylor1,5, Marcela Rosas1, Simon A Jones1, Sumukh Deshpande1, Robert Andrews1, Magdalena A Czubala1, Mark Gurney1, Maceler Aldrovandi1, Sven W Meckelmann1, Peter Ghazal1, Victor Darley-Usmar2, Daniel White1, and Valerie B O’Donnell1 1Systems Immunity Research Institute and Division of Infection and Immunity, and School of Medicine, Cardiff University, UK, 2Department of Pathology, University of Alabama at Birmingham, Birmingham, AL 35294, USA, 3Department of Pharmacology, University of Colorado Denver, Aurora, CO 80045, USA, 4Cayman Chemical 1180 E Ellsworth Rd, Ann Arbor, MI 48108, United States, 5UK Dementia Research Institute at Cardiff, Cardiff University, UK Address correspondence: Valerie O’Donnell, [email protected] or Daniel White, [email protected], Systems Immunity Research Institute, Cardiff University *Both authors contributed equally to the study 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.17.252007; this version posted November 3, 2020. 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.
  • Table 2. Significant

    Table 2. Significant

    Table 2. Significant (Q < 0.05 and |d | > 0.5) transcripts from the meta-analysis Gene Chr Mb Gene Name Affy ProbeSet cDNA_IDs d HAP/LAP d HAP/LAP d d IS Average d Ztest P values Q-value Symbol ID (study #5) 1 2 STS B2m 2 122 beta-2 microglobulin 1452428_a_at AI848245 1.75334941 4 3.2 4 3.2316485 1.07398E-09 5.69E-08 Man2b1 8 84.4 mannosidase 2, alpha B1 1416340_a_at H4049B01 3.75722111 3.87309653 2.1 1.6 2.84852656 5.32443E-07 1.58E-05 1110032A03Rik 9 50.9 RIKEN cDNA 1110032A03 gene 1417211_a_at H4035E05 4 1.66015788 4 1.7 2.82772795 2.94266E-05 0.000527 NA 9 48.5 --- 1456111_at 3.43701477 1.85785922 4 2 2.8237185 9.97969E-08 3.48E-06 Scn4b 9 45.3 Sodium channel, type IV, beta 1434008_at AI844796 3.79536664 1.63774235 3.3 2.3 2.75319499 1.48057E-08 6.21E-07 polypeptide Gadd45gip1 8 84.1 RIKEN cDNA 2310040G17 gene 1417619_at 4 3.38875643 1.4 2 2.69163229 8.84279E-06 0.0001904 BC056474 15 12.1 Mus musculus cDNA clone 1424117_at H3030A06 3.95752801 2.42838452 1.9 2.2 2.62132809 1.3344E-08 5.66E-07 MGC:67360 IMAGE:6823629, complete cds NA 4 153 guanine nucleotide binding protein, 1454696_at -3.46081884 -4 -1.3 -1.6 -2.6026947 8.58458E-05 0.0012617 beta 1 Gnb1 4 153 guanine nucleotide binding protein, 1417432_a_at H3094D02 -3.13334396 -4 -1.6 -1.7 -2.5946297 1.04542E-05 0.0002202 beta 1 Gadd45gip1 8 84.1 RAD23a homolog (S.
  • Environmental Influences on Endothelial Gene Expression

    Environmental Influences on Endothelial Gene Expression

    ENDOTHELIAL CELL GENE EXPRESSION John Matthew Jeff Herbert Supervisors: Prof. Roy Bicknell and Dr. Victoria Heath PhD thesis University of Birmingham August 2012 University of Birmingham Research Archive e-theses repository This unpublished thesis/dissertation is copyright of the author and/or third parties. The intellectual property rights of the author or third parties in respect of this work are as defined by The Copyright Designs and Patents Act 1988 or as modified by any successor legislation. Any use made of information contained in this thesis/dissertation must be in accordance with that legislation and must be properly acknowledged. Further distribution or reproduction in any format is prohibited without the permission of the copyright holder. ABSTRACT Tumour angiogenesis is a vital process in the pathology of tumour development and metastasis. Targeting markers of tumour endothelium provide a means of targeted destruction of a tumours oxygen and nutrient supply via destruction of tumour vasculature, which in turn ultimately leads to beneficial consequences to patients. Although current anti -angiogenic and vascular targeting strategies help patients, more potently in combination with chemo therapy, there is still a need for more tumour endothelial marker discoveries as current treatments have cardiovascular and other side effects. For the first time, the analyses of in-vivo biotinylation of an embryonic system is performed to obtain putative vascular targets. Also for the first time, deep sequencing is applied to freshly isolated tumour and normal endothelial cells from lung, colon and bladder tissues for the identification of pan-vascular-targets. Integration of the proteomic, deep sequencing, public cDNA libraries and microarrays, delivers 5,892 putative vascular targets to the science community.