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Gene set: COPD_UP_NING (C2:PERT:0105)
Standard nameCOPD_UP_NING
Systematic nameC2:PERT:0105
Brief descriptionUpregulated genes in lung tissue of smokers with chronic obstructive pulmonary disease (COPD) vs smokers without disease (GOLD-2 vs GOLD-0)
CategoryC2: Curated
Sub-categoryPERT: Experimental pertuberation
Full description or Abstract

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To better understand the molecular basis of chronic obstructive
pulmonary disease (COPD), we used serial analysis of gene expression
(SAGE) and microarray analysis to compare the gene expression
patterns of lung tissues from COPD and control smokers. A total
of 59,343 tags corresponding to 26,502 transcripts were sequenced
in SAGE analyses. A total of 327 genes were differentially expressed
(1.5-fold up- or down-regulated). Microarray analysis using the
same RNA source detected 261 transcripts that were differentially
expressed to a significant degree between GOLD-2 and GOLD-0 smokers.
We confirmed the altered expression of a select number of genes
by using real-time quantitative RT-PCR. These genes encode for
transcription factors (EGR1 and FOS), growth factors or related
proteins (CTGF, CYR61, CX3CL1, TGFB1, and PDGFRA), and extracellular
matrix protein (COL1A1). Immunofluorescence studies on the same
lung specimens localized the expression of Egr-1, CTGF, and Cyr61
to alveolar epithelial cells, airway epithelial cells, and stromal
and inflammatory cells of GOLD-2 smokers. Cigarette smoke extract
induced Egr-1 protein expression and increased Egr-1 DNA-binding
activity in human lung fibroblast cells. Cytomix (tumor necrosis
factor alpha, IL-1beta, and IFN-gamma) treatment showed that the
activity of matrix metalloproteinase-2 (MMP-2) was increased in
lung fibroblasts from EGR1 control (+/+) mice but not detected
in that of EGR1 null (-/-) mice, whereas MMP-9 was regulated by
EGR1 in a reverse manner. Our study represents the first comprehensive
analysis of gene expression on GOLD-2 versus GOLD-0 smokers and
reveals previously unreported candidate genes that may serve as
potential molecular targets in COPD. 
Publication URL15469929
External linksna
Keywords & MeSH headingsTranscription Factors/genetics,Immediate-Early Proteins/genetics,Middle Aged,Gene Expression Profiling,Oligonucleotide Array Sequence Analysis,P.H.S.,Lung/pathology,Humans,genetics,Gene Expression Regulation,Polymerase Chain Reaction,Smoking/pathology,Pulmonary Disease,physiology,DNA-Binding Proteins/genetics,Chronic Obstructive,physiopathology
OrganismHuman
Contributed byKate Stafford
Source platformGene_Symbol
Downloadgrp|xml|map
Genes

180 genes, 180 accessions (Toggle view)

GeneTitleLinks
RPL32ribosomal protein L32Source|GeneCards
RPS3ribosomal protein S3Source|GeneCards
H3F3BH3 histone, family 3B (H3.3B)Source|GeneCards
DCNdecorinSource|GeneCards
APOEapolipoprotein ESource|GeneCards
GK001GK001 proteinSource|GeneCards
CALM1calmodulin 1 (phosphorylase kinase, delta)Source|GeneCards
SNRP70small nuclear ribonucleoprotein 70kDa polypeptide (RNP antigen)Source|GeneCards
EGR1early growth response 1Source|GeneCards
RARRES2retinoic acid receptor responder (tazarotene induced) 2Source|GeneCards
PGDphosphogluconate dehydrogenaseSource|GeneCards
HIF3Ahypoxia inducible factor 3, alpha subunitSource|GeneCards
SNX4sorting nexin 4Source|GeneCards
TFF3trefoil factor 3 (intestinal)Source|GeneCards
TM4SF1transmembrane 4 superfamily member 1Source|GeneCards
RPLP0ribosomal protein, large, P0Source|GeneCards
VAMP8vesicle-associated membrane protein 8 (endobrevin)Source|GeneCards
PRO0628PRO0628 proteinSource|GeneCards
SFRS6splicing factor, arginine/serine-rich 6Source|GeneCards
RAMP3receptor (calcitonin) activity modifying protein 3Source|GeneCards
RPS15ribosomal protein S15Source|GeneCards
CLDN5claudin 5 (transmembrane protein deleted in velocardiofacial syndrome)Source|GeneCards
TNFSF10tumor necrosis factor (ligand) superfamily, member 10Source|GeneCards
TM4SF11transmembrane 4 superfamily member 11 (plasmolipin)Source|GeneCards
GPX4glutathione peroxidase 4 (phospholipid hydroperoxidase)Source|GeneCards
CKAP1cytoskeleton associated protein 1Source|GeneCards
ACTA1actin, alpha 1, skeletal muscleSource|GeneCards
A2Malpha-2-macroglobulinSource|GeneCards
MALmal, T-cell differentiation proteinSource|GeneCards
COL18A1collagen, type XVIII, alpha 1Source|GeneCards
TU3ATU3A proteinSource|GeneCards
CAPNS1calpain, small subunit 1Source|GeneCards
SERF2small EDRK-rich factor 2Source|GeneCards
ABCA8ATP-binding cassette, sub-family A (ABC1), member 8Source|GeneCards
C9ORF10chromosome 9 open reading frame 10Source|GeneCards
INPP1inositol polyphosphate-1-phosphataseSource|GeneCards
ILF3interleukin enhancer binding factor 3, 90kDaSource|GeneCards
ARCN1archain 1Source|GeneCards
WWP2Nedd-4-like ubiquitin-protein ligaseSource|GeneCards
APOFapolipoprotein FSource|GeneCards
RPL13ribosomal protein L13Source|GeneCards
CYR61cysteine-rich, angiogenic inducer, 61Source|GeneCards
CX3CL1chemokine (C-X3-C motif) ligand 1Source|GeneCards
G3BPRas-GTPase-activating protein SH3-domain-binding proteinSource|GeneCards
NUP43nucleoporin 43kDaSource|GeneCards
RPS23ribosomal protein S23Source|GeneCards
RABGGTBRab geranylgeranyltransferase, beta subunitSource|GeneCards
SUI1putative translation initiation factorSource|GeneCards
MAPK8IP1mitogen-activated protein kinase 8 interacting protein 1Source|GeneCards
VWFvon Willebrand factorSource|GeneCards
RARSarginyl-tRNA synthetaseSource|GeneCards
EPRSglutamyl-prolyl-tRNA synthetaseSource|GeneCards
PTP4A1protein tyrosine phosphatase type IVA, member 1Source|GeneCards
ATP5LATP synthase, H+ transporting, mitochondrial F0 complex, subunit gSource|GeneCards
MTCH1mitochondrial carrier homolog 1 (C. elegans)Source|GeneCards
UBE2E3ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast)Source|GeneCards
EGFL7EGF-like-domain, multiple 7Source|GeneCards
LGALS1lectin, galactoside-binding, soluble, 1 (galectin 1)Source|GeneCards
C22ORF19chromosome 22 open reading frame 19Source|GeneCards
DDX52DEAD (Asp-Glu-Ala-Asp) box polypeptide 52Source|GeneCards
CAPN3calpain 3, (p94)Source|GeneCards
COL4A1collagen, type IV, alpha 1Source|GeneCards
CTSFcathepsin FSource|GeneCards
FASNfatty acid synthaseSource|GeneCards
DGCR6DiGeorge syndrome critical region gene 6Source|GeneCards
GTF2Igeneral transcription factor II, iSource|GeneCards
OGDHoxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)Source|GeneCards
PTBP1polypyrimidine tract binding protein 1Source|GeneCards
SFRS10splicing factor, arginine/serine-rich 10 (transformer 2 homolog, Drosophila)Source|GeneCards
MRPL4mitochondrial ribosomal protein L4Source|GeneCards
SF1Splicing factor 1Source|GeneCards
INAinternexin neuronal intermediate filament protein, alphaSource|GeneCards
MRP63mitochondrial ribosomal protein 63Source|GeneCards
IL1R1interleukin 1 receptor, type ISource|GeneCards
NBL1neuroblastoma, suppression of tumorigenicity 1Source|GeneCards
MAT2Amethionine adenosyltransferase II, alphaSource|GeneCards
CPA3carboxypeptidase A3 (mast cell)Source|GeneCards
ALCAMactivated leukocyte cell adhesion moleculeSource|GeneCards
INMTindolethylamine N-methyltransferaseSource|GeneCards
NPC2Niemann-Pick disease, type C2Source|GeneCards
RPL14ribosomal protein L14Source|GeneCards
CDC42EP2CDC42 effector protein (Rho GTPase binding) 2Source|GeneCards
GNB2L1guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1Source|GeneCards
CYBRD1cytochrome b reductase 1Source|GeneCards
CSKc-src tyrosine kinaseSource|GeneCards
CGI-69CGI-69 proteinSource|GeneCards
MBD3methyl-CpG binding domain protein 3Source|GeneCards
HAX1HS1 binding proteinSource|GeneCards
NCKAP1NCK-associated protein 1Source|GeneCards
IGLJ3immunoglobulin lambda joining 3Source|GeneCards
FHOD1formin homology 2 domain containing 1Source|GeneCards
ITGA5integrin, alpha 5 (fibronectin receptor, alpha polypeptide)Source|GeneCards
C1ORF16chromosome 1 open reading frame 16Source|GeneCards
COPBcoatomer protein complex, subunit betaSource|GeneCards
CRI1CREBBP/EP300 inhibitory protein 1Source|GeneCards
HEYLhairy/enhancer-of-split related with YRPW motif-likeSource|GeneCards
SCO2SCO cytochrome oxidase deficient homolog 2 (yeast)Source|GeneCards
RPL4ribosomal protein L4Source|GeneCards
CTGFconnective tissue growth factorSource|GeneCards
TRIM8tripartite motif-containing 8Source|GeneCards
ACTN4actinin, alpha 4Source|GeneCards
SDC1syndecan 1Source|GeneCards
SPTAN1spectrin, alpha, non-erythrocytic 1 (alpha-fodrin)Source|GeneCards
SPIBSpi-B transcription factor (Spi-1/PU.1 related)Source|GeneCards
TGFBItransforming growth factor, beta-induced, 68kDaSource|GeneCards
ATP5BATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptideSource|GeneCards
C3Fputative protein similar to nessy (Drosophila)Source|GeneCards
DPYSL3dihydropyrimidinase-like 3Source|GeneCards
B4GALT5UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 5Source|GeneCards
GYPCglycophorin C (Gerbich blood group)Source|GeneCards
PNRC1proline-rich nuclear receptor coactivator 1Source|GeneCards
C1Rcomplement component 1, r subcomponentSource|GeneCards
NDUFA5NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5, 13kDaSource|GeneCards
TMSB10thymosin, beta 10Source|GeneCards
TPM2tropomyosin 2 (beta)Source|GeneCards
TNAtetranectin (plasminogen binding protein)Source|GeneCards
TGFB1transforming growth factor, beta 1 (Camurati-Engelmann disease)Source|GeneCards
FARP1FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)Source|GeneCards
HLA-Emajor histocompatibility complex, class I, ESource|GeneCards
BLVRAbiliverdin reductase ASource|GeneCards
PGM3phosphoglucomutase 3Source|GeneCards
SARA1SAR1a gene homolog 1 (S. cerevisiae)Source|GeneCards
CDH5cadherin 5, type 2, VE-cadherin (vascular epithelium)Source|GeneCards
IGFBP4insulin-like growth factor binding protein 4Source|GeneCards
GGTLA4gamma-glutamyltransferase-like activity 4Source|GeneCards
IGHMimmunoglobulin heavy constant muSource|GeneCards
MAF1homolog of yeast MAF1Source|GeneCards
MSLNmesothelinSource|GeneCards
GRINAglutamate receptor, ionotropic, N-methyl D-asparate-associated protein 1 (glutamate binding)Source|GeneCards
SSRP1structure specific recognition protein 1Source|GeneCards
WFS1Wolfram syndrome 1 (wolframin)Source|GeneCards
IGJimmunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptidesSource|GeneCards
OXA1Loxidase (cytochrome c) assembly 1-likeSource|GeneCards
ITPKBinositol 1,4,5-trisphosphate 3-kinase BSource|GeneCards
S100A9S100 calcium binding protein A9 (calgranulin B)Source|GeneCards
FGGfibrinogen, gamma polypeptideSource|GeneCards
TLE2transducin-like enhancer of split 2 (E(sp1) homolog, Drosophila)Source|GeneCards
KRT7keratin 7Source|GeneCards
PNMTPhenylethanolamine N-methyltransferaseSource|GeneCards
PKM2pyruvate kinase, muscleSource|GeneCards
BCAP31B-cell receptor-associated protein 31Source|GeneCards
RPL22ribosomal protein L22Source|GeneCards
FEZ2fasciculation and elongation protein zeta 2 (zygin II)Source|GeneCards
KLF2Kruppel-like factor 2 (lung)Source|GeneCards
PKD2polycystic kidney disease 2 (autosomal dominant)Source|GeneCards
HNRPA0heterogeneous nuclear ribonucleoprotein A0Source|GeneCards
PGLS6-phosphogluconolactonaseSource|GeneCards
MAPKAPK3mitogen-activated protein kinase-activated protein kinase 3Source|GeneCards
EIF4A1eukaryotic translation initiation factor 4A, isoform 1Source|GeneCards
ASPHaspartate beta-hydroxylaseSource|GeneCards
CDC2L1cell division cycle 2-like 1 (PITSLRE proteins)Source|GeneCards
RPL23Aribosomal protein L23aSource|GeneCards
DVL1dishevelled, dsh homolog 1 (Drosophila)Source|GeneCards
RPLP1ribosomal protein, large, P1Source|GeneCards
FOSv-fos FBJ murine osteosarcoma viral oncogene homologSource|GeneCards
LAPTM5Lysosomal-associated multispanning membrane protein-5Source|GeneCards
CDKN1Acyclin-dependent kinase inhibitor 1A (p21, Cip1)Source|GeneCards
EDF1endothelial differentiation-related factor 1Source|GeneCards
ATP5DATP synthase, H+ transporting, mitochondrial F1 complex, delta subunitSource|GeneCards


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