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Supplementary Table S1 . 939 Differentially Expressed Genes in Invasive Cells with EGFR Over-Expression and P53 Mutation

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Supplementary Table S1 . 939 Differentially Expressed Genes in Invasive Cells with EGFR Over-expression and P53 Mutation AffyID Gene Fold Chromosomal_Location Gene_Title Change* 210809_s_at POSTN 6.54 chr13q13.3 periostin, osteoblast specific factor 202237_at NNMT 5.76 chr11q23.1 nicotinamide N-methyltransferase 226237_at COL8A1 5.43 --- --- 58780_s_at FLJ10357 5.41 chr14q11.2 hypothetical protein FLJ10357 201109_s_at THBS1 5.11 chr15q15 thrombospondin 1 213905_x_at BGN 5.07 chrXq28 biglycan 229125_at LOC163782 4.79 chr1p31.3 KN motif and ankyrin repeat domains 4 209278_s_at TFPI2 4.64 chr7q22 tissue factor pathway inhibitor 2 202766_s_at FBN1 4.63 chr15q21.1 fibrillin 1 204955_at SRPX 4.61 chrXp21.1 sushi-repeat-containing protein, X-linked 204083_s_at TPM2 4.44 chr9p13.2-p13.1 tropomyosin 2 (beta) 212473_s_at MICAL2 4.34 chr11p15.3 microtubule associated monoxygenase, calponin and LIM domain containing 2 211964_at COL4A2 4.28 chr13q34 collagen, type IV, alpha 2 201261_x_at BGN 4.28 chrXq28 biglycan 216250_s_at LPXN 4.17 chr11q12.1 leupaxin 209651_at TGFB1I1 4.15 chr16p11.2 transforming growth factor beta 1 induced transcript 1 226905_at MGC45871 4.15 chr17p13 family with sequence similarity 101, member B 201431_s_at DPYSL3 4.14 chr5q32 dihydropyrimidinase-like 3 200974_at ACTA2 4.10 chr10q23.3 actin, alpha 2, smooth muscle, aorta 226876_at MGC45871 4.09 chr17p13 family with sequence similarity 101, member B 206300_s_at PTHLH 4.01 chr12p12.1-p11.2 parathyroid hormone-like hormone 227566_at HNT 3.98 chr11q25 neurotrimin 201110_s_at THBS1 3.94 chr15q15 thrombospondin 1 210511_s_at INHBA 3.93 chr7p15-p13 inhibin, beta A 225681_at CTHRC1 3.84 chr8q22.3 collagen triple helix repeat containing 1 44783_s_at HEY1 3.84 chr8q21 hairy/enhancer-of-split related with YRPW motif 1 202686_s_at AXL 3.80 chr19q13.1 AXL receptor tyrosine kinase 206247_at MICB 3.78 chr6p21.3 MHC class I polypeptide-related sequence B 227059_at GPC6 3.73 chr13q32 glypican 6 201162_at IGFBP7 3.72 chr4q12 insulin-like growth factor binding protein 7 212667_at SPARC 3.72 chr5q31.3-q32 secreted protein, acidic, cysteine-rich (osteonectin) 231766_s_at COL12A1 3.67 chr6q12-q13 collagen, type XII, alpha 1 212472_at MICAL2 3.63 chr11p15.3 microtubule associated monoxygenase, calponin and LIM domain containing 2 201108_s_at THBS1 3.61 chr15q15 thrombospondin 1 213869_x_at THY1 3.60 chr11q22.3-q23 Thy-1 cell surface antigen 203925_at GCLM 3.58 chr1p22.1 glutamate-cysteine ligase, modifier subunit 212609_s_at SDCCAG8 3.58 chr1q43-q44 Clones 23920 and 23921 mRNA sequence 1556773_at PTHLH 3.53 --- --- 221059_s_at CHST6 3.52 chr16q24.1 coactosin-like 1 (Dictyostelium) 211980_at COL4A1 3.51 chr13q34 collagen, type IV, alpha 1 201389_at ITGA5 3.50 chr12q11-q13 integrin, alpha 5 (fibronectin receptor, alpha polypeptide) 202760_s_at AKAP2 3.47 chr9q31-q33 PALM2-AKAP2 readthrough transcript 229218_at COL1A2 3.47 chr7q22.1 collagen, type I, alpha 2 212013_at D2S448 3.46 chr2p25 peroxidasin homolog (Drosophila) 201645_at TNC 3.44 chr9q33 tenascin C 210355_at PTHLH 3.43 chr12p12.1-p11.2 parathyroid hormone-like hormone 203562_at FEZ1 3.37 chr11q24.2 fasciculation and elongation protein zeta 1 (zygin I) 206580_s_at EFEMP2 3.36 chr11q13.1 EGF-containing fibulin-like extracellular matrix protein 2 201666_at TIMP1 3.34 chrXp11.3-p11.23 TIMP metallopeptidase inhibitor 1 213010_at PRKCDBP 3.31 chr11p15.4 protein kinase C, delta binding protein 228033_at E2F7 3.31 chr12q21.2 E2F transcription factor 7 224911_s_at DCBLD2 3.31 chr3q12.1|3 discoidin, CUB and LCCL domain containing 2 204115_at GNG11 3.30 chr7q21 guanine nucleotide binding protein (G protein), gamma 11 202759_s_at AKAP2 chr9q31-q33 A kinase (PRKA) anchor protein 2 /// paralemmin 2 /// PALM2-AKAP2 readthrough transcript 3.30 226694_at AKAP2 chr9q31-q33 A kinase (PRKA) anchor protein 2 /// paralemmin 2 /// PALM2-AKAP2 readthrough transcript 3.30 204464_s_at EDNRA 3.30 chr4q31.23 endothelin receptor type A 225664_at COL12A1 3.29 chr6q12-q13 collagen, type XII, alpha 1 209270_at LAMB3 3.27 chr1q32 laminin, beta 3 212233_at MAP1B 3.26 chr5q13 microtubule-associated protein 1B 225524_at ANTXR2 3.24 chr4q21.21 anthrax toxin receptor 2 209210_s_at PLEKHC1 3.24 chr14q22.2 fermitin family homolog 2 (Drosophila) 212624_s_at CHN1 3.23 chr2q31.1 chimerin (chimaerin) 1 209277_at TFPI2 3.22 chr7q22 tissue factor pathway inhibitor 2 206467_x_at TNFRSF6B chr20q13.3 regulator of telomere elongation helicase 1 /// tumor necrosis factor receptor superfamily, member 3.22 6b, decoy 217853_at TENS1 3.21 chr7p12.3 tensin 3 214085_x_at GLIPR1 3.19 chr12q21.2 GLI pathogenesis-related 1 207826_s_at ID3 3.18 chr1p36.13-p36.12 inhibitor of DNA binding 3, dominant negative helix-loop-helix protein 212489_at COL5A1 3.17 chr9q34.2-q34.3 collagen, type V, alpha 1 208962_s_at FADS1 3.16 chr11q12.2-q13.1 fatty acid desaturase 1 202998_s_at LOXL2 3.15 chr8p21.3 /// chr8p21.3-p21.2 ectonucleoside triphosphate diphosphohydrolase 4 /// lysyl oxidase-like 2 202270_at GBP1 3.10 chr1p22.2 guanylate binding protein 1, interferon-inducible, 67kDa 225673_at MYADM 3.10 chr19q13.41 myeloid-associated differentiation marker 230175_s_at ESDN 3.08 --- --- 201105_at LGALS1 3.06 chr22q13.1 lectin, galactoside-binding, soluble, 1 202870_s_at CDC20 3.05 chr1p34.1 cell division cycle 20 homolog (S. cerevisiae) 227534_at C9orf21 3.03 chr9q22.32 chromosome 9 open reading frame 21 52255_s_at COL5A3 3.02 chr19p13.2 collagen, type V, alpha 3 238447_at RBMS3 3.02 chr3p24-p23 RNA binding motif, single stranded interacting protein 214104_at GPR161 3.00 chr1q24.2 G protein-coupled receptor 161 204030_s_at SCHIP1 3.00 chr3q25.33 schwannomin interacting protein 1 211756_at PTHLH 2.99 chr12p12.1-p11.2 parathyroid hormone-like hormone 65718_at GPR124 2.98 chr8p12 G protein-coupled receptor 124 203217_s_at SIAT9 2.97 chr2p11.2 ST3 beta-galactoside alpha-2,3-sialyltransferase 5 223307_at CDCA3 2.96 chr12p13 cell division cycle associated 3 205120_s_at SGCB 2.94 chr4q12 sarcoglycan, beta (43kDa dystrophin-associated glycoprotein) 221916_at NEFL 2.93 chr8p21 neurofilament, light polypeptide 212464_s_at FN1 2.93 chr2q34 fibronectin 1 218651_s_at FLJ11196 2.90 chr15q23 La ribonucleoprotein domain family, member 6 204682_at LTBP2 2.89 chr14q24 latent transforming growth factor beta binding protein 2 219117_s_at FKBP11 2.89 chr12q13.12 FK506 binding protein 11, 19 kDa 1555630_a_at RAB34 2.88 chr17q11.2 RAB34, member RAS oncogene family 37408_at MRC2 2.87 chr17q23.2 mannose receptor, C type 2 210987_x_at TPM1 2.87 chr15q22.1 tropomyosin 1 (alpha) 219257_s_at SPHK1 2.86 chr17q25.2 sphingosine kinase 1 228573_at ANTXR2 2.84 --- --- 203060_s_at PAPSS2 2.82 chr10q23-q24 3'-phosphoadenosine 5'-phosphosulfate synthase 2 212022_s_at MKI67 2.81 chr10q25-qter antigen identified by monoclonal antibody Ki-67 227279_at MGC15737 2.80 chrXq22.2 transcription elongation factor A (SII)-like 3 201163_s_at IGFBP7 2.80 chr4q12 insulin-like growth factor binding protein 7 211340_s_at MCAM 2.79 chr11q23.3 melanoma cell adhesion molecule 213943_at TWIST1 2.79 chr7p21.2 twist homolog 1 (Drosophila) 202267_at LAMC2 2.76 chr1q25-q31 laminin, gamma 2 224759_s_at MGC17943 2.76 chr12q23.3 chromosome 12 open reading frame 23 218638_s_at SPON2 2.74 chr4p16.3 spondin 2, extracellular matrix protein 209946_at VEGFC 2.73 chr4q34.1-q34.3 vascular endothelial growth factor C 212607_at AKT3 2.72 chr1q43-q44 v-akt murine thymoma viral oncogene homolog 3 (protein kinase B, gamma) 221805_at NEFL 2.72 chr8p21 neurofilament, light polypeptide 208637_x_at ACTN1 2.72 chr14q24.1-q24.2|14q24|14q22-q24 actinin, alpha 1 222108_at AMIGO2 2.71 chr12q13.11 adhesion molecule with Ig-like domain 2 211160_x_at ACTN1 2.71 chr14q24.1-q24.2|14q24|14q22-q24 actinin, alpha 1 213262_at SACS 2.70 chr13q12 spastic ataxia of Charlevoix-Saguenay (sacsin) 218656_s_at LHFP 2.70 chr13q12 lipoma HMGIC fusion partner 200762_at DPYSL2 2.69 chr8p22-p21 dihydropyrimidinase-like 2 208851_s_at THY1 2.69 chr11q22.3-q23 Thy-1 cell surface antigen 224833_at ETS1 2.69 chr11q23.3 v-ets erythroblastosis virus E26 oncogene homolog 1 (avian) 205534_at PCDH7 2.66 chr4p15 protocadherin 7 224252_s_at FXYD5 2.66 chr19q12-q13.1 FXYD domain containing ion transport regulator 5 229404_at TWIST2 2.65 chr2q37.3 twist homolog 2 (Drosophila) 227211_at PHF19 2.64 chr9q33.2 PHD finger protein 19 209335_at DCN 2.64 chr12q21.33 decorin 223378_at GLIS2 2.62 chr16p13.3 GLIS family zinc finger 2 204466_s_at SNCA 2.61 chr4q21 synuclein, alpha (non A4 component of amyloid precursor) 201843_s_at EFEMP1 2.61 chr2p16 EGF-containing fibulin-like extracellular matrix protein 1 216442_x_at FN1 2.59 chr2q34 fibronectin 1 208963_x_at FADS1 2.58 chr11q12.2-q13.1 fatty acid desaturase 1 208964_s_at FADS1 2.58 chr11q12.2-q13.1 fatty acid desaturase 1 204279_at PSMB9 chr6p21.3 proteasome (prosome, macropain) subunit, beta type, 9 (large multifunctional peptidase 2) 2.58 210495_x_at FN1 2.57 chr2q34 fibronectin 1 212110_at SLC39A14 2.57 chr8p21.3 solute carrier family 39 (zinc transporter), member 14 213069_at HEG 2.57 chr3q21.2 HEG homolog 1 (zebrafish) 219305_x_at FBXO2 2.56 chr1p36.22 F-box protein 2 227759_at PCSK9 2.56 chr1p32.3 proprotein convertase subtilisin/kexin type 9 202555_s_at MYLK 2.56 chr3q21 myosin light chain kinase 218980_at FHOD3 2.56 chr18q12 formin homology 2 domain containing 3 218368_s_at TNFRSF12A 2.55 chr16p13.3 tumor necrosis factor receptor superfamily, member 12A 214710_s_at CCNB1 2.55 chr5q12 cyclin B1 224710_at RAB34 2.54 chr17q11.2 RAB34, member RAS oncogene family 202206_at
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    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,
  • Wnt/Β-Catenin Signaling Regulates Regeneration in Diverse Tissues of the Zebrafish

    Wnt/Β-Catenin Signaling Regulates Regeneration in Diverse Tissues of the Zebrafish

    Wnt/β-catenin Signaling Regulates Regeneration in Diverse Tissues of the Zebrafish Nicholas Stockton Strand A dissertation Submitted in partial fulfillment of the Requirements for the degree of Doctor of Philosophy University of Washington 2016 Reading Committee: Randall Moon, Chair Neil Nathanson Ronald Kwon Program Authorized to Offer Degree: Pharmacology ©Copyright 2016 Nicholas Stockton Strand University of Washington Abstract Wnt/β-catenin Signaling Regulates Regeneration in Diverse Tissues of the Zebrafish Nicholas Stockton Strand Chair of the Supervisory Committee: Professor Randall T Moon Department of Pharmacology The ability to regenerate tissue after injury is limited by species, tissue type, and age of the organism. Understanding the mechanisms of endogenous regeneration provides greater insight into this remarkable biological process while also offering up potential therapeutic targets for promoting regeneration in humans. The Wnt/β-catenin signaling pathway has been implicated in zebrafish regeneration, including the fin and nervous system. The body of work presented here expands upon the role of Wnt/β-catenin signaling in regeneration, characterizing roles for Wnt/β-catenin signaling in multiple tissues. We show that cholinergic signaling is required for blastema formation and Wnt/β-catenin signaling initiation in the caudal fin, and that overexpression of Wnt/β-catenin ligand is sufficient to rescue blastema formation in fins lacking cholinergic activity. Next, we characterized the glial response to Wnt/β-catenin signaling after spinal cord injury, demonstrating that Wnt/β-catenin signaling is necessary for recovery of motor function and the formation of bipolar glia after spinal cord injury. Lastly, we defined a role for Wnt/β-catenin signaling in heart regeneration, showing that cardiomyocyte proliferation is regulated by Wnt/β-catenin signaling.
  • Dietary Protein Restriction Rapidly Reduces Transforming Growth Factor

    Dietary Protein Restriction Rapidly Reduces Transforming Growth Factor

    Proc. Natl. Acad. Sci. USA Vol. 88, pp. 9765-9769, November 1991 Medical Sciences Dietary protein restriction rapidly reduces transforming growth factor p1 expression in experimental glomerulonephritis (extraceliular matrix/transforming growth factor 8/glomerulonephritis) SEIYA OKUDA*, TAKAMICHI NAKAMURA*, TATSUO YAMAMOTO*, ERKKI RUOSLAHTIt, AND WAYNE A. BORDER*t *Division of Nephrology, University of Utah School of Medicine, Salt Lake City, UT 84132; and tCancer Research Center, La Jolla Cancer Research Foundation, La Jolla, CA 92037 Communicated by Eugene Roberts, August 19, 1991 (receivedfor review April 29, 1991) ABSTRACT Dietary protein restriction has been shown to TGF-/31 on both cell types is to regulate the synthesis of two slow the rate of loss of kidney function in humans with chondroitin/dermatan sulfate proteoglycans, biglycan and progressive glomerulosclerosis due to glomerulonephritis or decorin, both of which can bind TGF-P1 (23). In an experi- diabetes mellitus. A central feature of glomerulosclerosis is the mental model ofglomerulonephritis in the rat, we have found pathological accumulation of extracellular matrix within the a close association between elevated expression of the diseased glomeruli. Transforming growth factor j1 (TGF-.81) TGF-131 gene and the development of glomerulonephritis is known to have widespread regulatory effects on extracellular (10). Seven days after glomerular injury, at the time of matrix and has been implicated as a major cause of increased significant extracellular matrix accumulation, the glomeruli extracellular matrix synthesis and buildup of pathological showed a 5-fold increase in TGF-f31 mRNA and a nearly matrix within glomeruli in experimental glomerulonephritis. 50-fold increase in production ofbiglycan and decorin.
  • Plakophilin-2 Haploinsufficiency Causes Calcium Handling

    Plakophilin-2 Haploinsufficiency Causes Calcium Handling

    International Journal of Molecular Sciences Article Plakophilin-2 Haploinsufficiency Causes Calcium Handling Deficits and Modulates the Cardiac Response Towards Stress Chantal J.M. van Opbergen 1 , Maartje Noorman 1, Anna Pfenniger 2, Jaël S. Copier 1, Sarah H. Vermij 2,3 , Zhen Li 2, Roel van der Nagel 1, Mingliang Zhang 2, Jacques M.T. de Bakker 1,4, Aaron M. Glass 5, Peter J. Mohler 6,7, Steven M. Taffet 5, Marc A. Vos 1, Harold V.M. van Rijen 1, Mario Delmar 2 and Toon A.B. van Veen 1,* 1 Department of Medical Physiology, Division of Heart & Lungs, University Medical Center Utrecht, Yalelaan 50, 3584CM Utrecht, The Netherlands 2 Division of Cardiology, NYU School of Medicine, New York, NY 10016, USA 3 Institute of Biochemistry and Molecular Medicine, University of Bern, 3012 Bern, Switzerland 4 Department of Medical Biology, Academic Medical Center Amsterdam, 1105AZ Amsterdam, The Netherlands 5 Department of Microbiology and Immunology, SUNY Upstate Medical University, Syracuse, NY 13210, USA 6 Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University College of Medicine and Wexner Medical Center, Columbus, OH 43210, USA 7 Departments of Physiology & Cell Biology and Internal Medicine, Division of Cardiovascular Medicine, The Ohio State University College of Medicine Wexner Medical Center, Columbus, OH 43210, USA * Correspondence: [email protected] Received: 1 August 2019; Accepted: 19 August 2019; Published: 21 August 2019 Abstract: Human variants in plakophilin-2 (PKP2) associate with most cases of familial arrhythmogenic cardiomyopathy (ACM). Recent studies show that PKP2 not only maintains intercellular coupling, but also regulates transcription of genes involved in Ca2+ cycling and cardiac rhythm.