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Supplemental Table 1. Genes activated by alcohol in cultured cortical neurons, as assessed by micro-array analysis. Gene Description Genbank Acc No Folds of increase Gpnmb glycoprotein (transmembrane) nmb NM_053110 2.58 Lyzs lysozyme NM_017372 2.36 Gpnmb glycoprotein (transmembrane) nmb NM_053110 2.33 Gpnmb glycoprotein (transmembrane) nmb NM_053110 2.27 Gpm6a glycoprotein m6a NM_153581 2.05 Mtap1b microtubule-associated protein 1 B NM_008634 2.00 Gfap glial fibrillary acidic protein NM_010277 1.94 C1qg complement component 1, q subcomponent, C chain NM_007574 1.90 C1qb complement component 1, q subcomponent, beta polypeptide, mRNA NM_009777 1.87 Laptm5 lysosomal-associated protein transmembrane 5 NM_010686 1.82 Apoc1 apolipoprotein C-I NM_007469 1.81 Lgals3 lectin, galactose binding, soluble 3 NM_010705 1.81 Fcer1g Fc receptor, IgE, high affinity I, gamma polypeptide NM_010185 1.81 Cd68 CD68 antigen NM_009853 1.81 Apoe apolipoprotein E NM_009696 1.76 C1qa complement component 1, q subcomponent, alpha polypeptide NM_007572 1.75 Lgmn legumain NM_011175 1.74 Msr2 macrophage scavenger receptor 2 NM_030707 1.72 Trem2 triggering receptor expressed on myeloid cells 2 NM_031254 1.72 Serpina3n serine (or cysteine) peptidase inhibitor, clade A, member 3N NM_009252 1.71 Igf1 insulin-like growth factor 1, transcript variant 1 NM_010512 1.71 Ctsz cathepsin Z NM_022325 1.71 Adfp adipose differentiation related protein NM_007408 1.69 Pdgfra platelet derived growth factor receptor, alpha polypeptide NM_011058 1.67 Mmp12 matrix metallopeptidase 12 NM_008605 1.66 Nrgn neurogranin NM_022029 1.65 4831417L10 ELMO domain containing 1 NM_177769 1.64 Cyba cytochrome b-245, alpha polypeptide NM_007806 1.63 Eef2 eukaryotic translation elongation factor 2 NM_007907 1.63 Ctsb cathepsin B NM_007798 1.62 Bcl2a1a B-cell leukemia/lymphoma 2 related protein A1b NM_007534 1.61 Apoc1 apolipoprotein C-I NM_007469 1.61 Abcg1 ATP-binding cassette, sub-family G (WHITE), member 1 NM_009593 1.61 Igf1 insulin-like growth factor 1, transcript variant 2 NM_184052 1.59 Trf transferrin NM_133977 1.57 elf1; elf3 spectrin beta 2, transcript variant 1 NM_175836 1.57 Hnrpk heterogeneous nuclear ribonucleoprotein K NM_025279 1.57 Mtap1b microtubule-associated protein 1 B NM_008634 1.57 Gpc5 glypican 5 NM_175500 1.57 Grn granulin NM_008175 1.57 Fcgr3 Fc receptor, IgG, low affinity III NM_010188 1.56 Bcl2a1d B-cell leukemia/lymphoma 2 related protein A1d NM_007536 1.55 Lpl lipoprotein lipase NM_008509 1.54 1 Sec23a SEC23A (S. cerevisiae) NM_009147 1.53 Ly86 lymphocyte antigen 86 NM_010745 1.53 Syt1 synaptotagmin I NM_009306 1.53 Cdh13 cadherin 13 NM_019707 1.52 Blnk B-cell linker NM_008528 1.52 Sgk serum/glucocorticoid regulated kinase NM_011361 1.51 Igf1 insulin-like growth factor 1, transcript variant 1 NM_010512 1.51 2 Supplemental Table 2. Genes activated by heat shock in cultured cortical neurons, as assessed by micro-array analysis. Gene Description Genbank Acc No Ranking Gucy1a3 guanylate cyclase 1, soluble, alpha 3 (Gucy1a3) NM_021896 3.34 Sv2b synaptic vesicle glycoprotein 2 b (Sv2b), NM_153579 3.10 Dfy Duffy blood group, chemokine receptor (Darc) NM_010045 2.58 Fst follistatin (Fst) NM_008046 2.58 Gucy1a3 guanylate cyclase 1, soluble, alpha 3 (Gucy1a3) NM_021896 2.57 Gpc5 glypican 5 (Gpc5), NM_175500 2.39 Gucy1b3 guanylate cyclase 1, soluble, beta 3 (Gucy1b3) NM_017469 2.38 Nrgn neurogranin (Nrgn) NM_022029 2.38 Tes testis derived transcript (Tes) NM_011570 2.37 Gucy1a3 guanylate cyclase 1, soluble, alpha 3 (Gucy1a3) NM_021896 2.36 3110047P20Rik RIKEN cDNA 3110047P20 gene (3110047P20Rik XM_132047 2.33 Gpr88 G-protein coupled receptor 88 (Gpr88) NM_022427 2.31 Nef3 neurofilament, medium polypeptide (Nefm), NM_008691 2.26 Cbln1 cerebellin 1 precursor protein (Cbln1 NM_019626 2.26 Ttr transthyretin (Ttr), NM_013697 2.24 Efcbp1 EF hand calcium binding protein 1 (Efcbp1), NM_178617 2.23 Pcsk2 proprotein convertase subtilisin/kexin type 2 (Pcsk2), NM_008792 2.22 Spnb3 spectrin beta 3 (Spnb3 XM_129130 2.18 Cdh13 cadherin 13 (Cdh13), NM_019707 2.18 Syt1 synaptotagmin I (Syt1) NM_009306 2.15 Cdh13 cadherin 13 (Cdh13), NM_019707 2.15 Nnat neuronatin (Nnat) NM_010923 2.15 4831417L10 domain containing 1 (Elmod1) NM_177769 2.10 Stmn4 stathmin-like 4 (Stmn4) NM_019675 2.10 Dmn desmuslin (Dmn) NM_207663 2.09 Caln1 calneuron 1 (Caln1) NM_021371 2.09 Prss12 protease, serine, 12 neurotrypsin (motopsin) (Prss12) NM_008939 2.09 Ngef neuronal guanine nucleotide exchange factor (Ngef) NM_019867 2.08 Spock1 sparc/osteonectin, cwcv and kazal-like domains proteoglycan 1 (Spock1) NM_009262 2.06 Hpca hippocalcin (Hpca) NM_010471 2.05 Rac3 RAS-related C3 botulinum substrate 3 (Rac3) NM_133223 2.05 DNA segment, Chr 3, Brigham & Women's Genetics 0562 expressed D3Bwg0562e (D3Bwg0562e) NM_177664 2.05 Ntf3 neurotrophin 3 (Ntf3) NM_008742 2.03 Ppp2r2c protein phosphatase 2, regulatory subunit B (PR 52), gamma isoform (Ppp2r2c) NM_172994 2.01 Syt4 synaptotagmin IV (Syt4) NM_009308 2.00 Epha8 Eph receptor A8 (Epha8) NM_007939 2.00 Zfp537 teashirt zinc finger family member 3 (Tshz3) NM_172298 1.99 Chst8 carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8 (Chst8) NM_175140 1.99 Zfp238 zinc finger protein 238 (Zfp238) NM_013915 1.99 AI836003 expressed sequence AI836003 (AI836003) NM_177716 1.98 Slc29a4 solute carrier family 29 (nucleoside transporters), member 4 (Slc29a4) NM_146257 1.98 5330439J01Rik cDNA 5330439J01 gene (5330439J01Rik) NM_175407 1.98 Tes testis derived transcript (Tes) NM_011570 1.98 3 D6Ertd365e zinc and ring finger 2 (Znrf2) NM_199143 1.97 Akt3 thymoma viral proto-oncogene 3 (Akt3) NM_011785 1.97 Tubb4 tubulin, beta 4 (Tubb4) NM_009451 1.97 1700001L19Rik cDNA 1700001L19 gene (1700001L19Rik) XM_127414 1.96 Arrdc4 arrestin domain containing 4 (Arrdc4) NM_025549 1.96 Dmn desmuslin (Dmn) NM_207663 1.94 Ldb2 LIM domain binding 2 (Ldb2) NM_010698 1.94 Smpd3 sphingomyelin phosphodiesterase 3, neutral NM_021491 1.94 Flrt3 fibronectin leucine rich transmembrane protein 3 NM_178382 1.94 Vsnl1 visinin-like 1 NM_012038 1.93 Ldb2 LIM domain binding 2 (Ldb2), transcript variant 1 NM_010698 1.93 Acat2 acetyl-Coenzyme A acetyltransferase 2 NM_009338 1.93 Wsb2 WD repeat and SOCS box-containing 2 NM_021539 1.93 Rab15 RAB15, member RAS oncogene family NM_134050 1.90 Brunol4 bruno-like 4, RNA binding protein (Drosophila) NM_133195 1.89 Emid2 EMI domain containing 2 NM_024474 1.89 elf1; elf3 spectrin beta 2 (Spnb2), transcript variant 1 NM_175836 1.89 3110006E14Rik cDNA 3110006E14 gene (3110006E14Rik) XM_127466 1.88 Lrrn3 leucine rich repeat protein 3, neuronal (Lrrn3) NM_010733 1.88 Slc2a6 solute carrier family 2 (facilitated glucose transporter), member 6 NM_172659 1.88 BC017634 CaM kinase-like vesicle-associated NM_145621 1.87 Lor loricrin NM_008508 1.87 Enc1 ectodermal-neural cortex 1 NM_007930 1.86 Crmp1 collapsin response mediator protein 1 NM_007765 1.86 Cobl cordon-bleu NM_172496 1.86 Sncb synuclein, beta NM_033610 1.86 Neurl neuralized-like homolog (Drosophila) NM_021360 1.85 Bach acyl-CoA thioesterase 7 NM_133348 1.84 Mtap1b microtubule-associated protein 1 B NM_008634 1.84 Nudt4 nudix (nucleoside diphosphate linked moiety X)-type motif 4 NM_027722 1.84 Aacs acetoacetyl-CoA synthetase NM_030210 1.84 Atp9a ATPase, class II, type 9A NM_015731 1.84 Stx1a syntaxin 1A ( NM_016801 1.83 Neo1 neogenin (Neo1), transcript variant 1 NM_008684 1.83 Slco3a1 solute carrier organic anion transporter family, member 3a1 NM_023908 1.83 Ncald neurocalcin delta NM_134094 1.83 Nsdhl NAD(P) dependent steroid dehydrogenase-like NM_010941 1.83 Arhgdig Rho GDP dissociation inhibitor (GDI) gamma NM_008113 1.83 Sqle squalene epoxidase NM_009270 1.83 Eef1a2 eukaryotic translation elongation factor 1 alpha 2 NM_007906 1.82 Syn1 synapsin I NM_013680 1.82 Prkcz protein kinase C, zeta (Prkcz), transcript variant 1 NM_008860 1.82 AI593442 expressed sequence AI593442 (AI593442), transcript variant 1 NM_177907 1.82 4930420O11Rik Mus musculus microtubule associated serine/threonine kinase family XM_283179 1.82 Slc17a6 solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter) NM_080853 1.82 Nsdhl NAD(P) dependent steroid dehydrogenase-like NM_010941 1.81 Lrfn2 leucine rich repeat and fibronectin type III domain containing 2 NM_027452 1.81 4 Atp9a ATPase, class II, type 9A NM_015731 1.81 Fdps farnesyl diphosphate synthetase NM_134469 1.81 Scn3b sodium channel, voltage-gated, type III, beta (Scn3b), transcript variant 2 NM_178227 1.81 Satb2 special AT-rich sequence binding protein 2 NM_139146 1.81 Cdkl2 cyclin-dependent kinase-like 2 (CDC2-related kinase) NM_177270 1.81 Mef2c myocyte enhancer factor 2C NM_025282 1.81 Slc6a17 solute carrier family 6 (neurotransmitter transporter), member 17 NM_172271 1.81 Gprin1 G protein-regulated inducer of neurite outgrowth 1 NM_012014 1.80 Wdr47 WD repeat domain 47 NM_181400 1.80 Met met proto-oncogene NM_008591 1.80 Jakmip1 janus kinase and microtubule interacting protein 1 NM_178394 1.80 Chst1 carbohydrate (keratan sulfate Gal-6) sulfotransferase 1 NM_023850 1.80 Acat2 acetyl-Coenzyme A acetyltransferase 2 NM_009338 1.79 D15Bwg0669e metallophosphoesterase domain containing 1 NM_172610 1.79 Nsdhl NAD(P) dependent steroid dehydrogenase-like NM_010941 1.79 Ly6h lymphocyte antigen 6 complex, locus H NM_011837 1.78 Igsf4b cell adhesion molecule 3 NM_053199 1.78 Sertad4 SERTA domain containing 4 NM_198247 1.78 Hmgcr 3-hydroxy-3-methylglutaryl-Coenzyme A reductase NM_008255 1.78 Gnao1 guanine nucleotide binding protein, alpha o NM_010308 1.77 Pou3f1 POU domain, class
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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,
  • Ten Commandments for a Good Scientist

    Ten Commandments for a Good Scientist

    Unravelling the mechanism of differential biological responses induced by food-borne xeno- and phyto-estrogenic compounds Ana María Sotoca Covaleda Wageningen 2010 Thesis committee Thesis supervisors Prof. dr. ir. Ivonne M.C.M. Rietjens Professor of Toxicology Wageningen University Prof. dr. Albertinka J. Murk Personal chair at the sub-department of Toxicology Wageningen University Thesis co-supervisor Dr. ir. Jacques J.M. Vervoort Associate professor at the Laboratory of Biochemistry Wageningen University Other members Prof. dr. Michael R. Muller, Wageningen University Prof. dr. ir. Huub F.J. Savelkoul, Wageningen University Prof. dr. Everardus J. van Zoelen, Radboud University Nijmegen Dr. ir. Toine F.H. Bovee, RIKILT, Wageningen This research was conducted under the auspices of the Graduate School VLAG Unravelling the mechanism of differential biological responses induced by food-borne xeno- and phyto-estrogenic compounds Ana María Sotoca Covaleda Thesis submitted in fulfillment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. dr. M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Tuesday 14 September 2010 at 4 p.m. in the Aula Unravelling the mechanism of differential biological responses induced by food-borne xeno- and phyto-estrogenic compounds. Ana María Sotoca Covaleda Thesis Wageningen University, Wageningen, The Netherlands, 2010, With references, and with summary in Dutch. ISBN: 978-90-8585-707-5 “Caminante no hay camino, se hace camino al andar. Al andar se hace camino, y al volver la vista atrás se ve la senda que nunca se ha de volver a pisar” - Antonio Machado – A mi madre.
  • G Protein-Coupled Receptors

    G Protein-Coupled Receptors

    www.aladdin-e.com Address:800 S Wineville Avenue, Ontario, CA 91761,USA Website:www.aladdin-e.com Email USA: [email protected] Email EU: [email protected] Email Asia Pacific: [email protected] G PROTEIN-COUPLED RECEPTORS Overview: The completion of the Human Genome Project allowed the identification of a large family of proteins with a common motif of seven groups of 20–24 hydrophobic amino acids arranged as a-helices. Approximately 800 of these seven transmembrane (7TM) receptors have been identified of which over 300 are non-olfactory receptors (see Fredriksson et al., 2003; Lagerstrom and Schioth, 2008). Subdivision on the basis of sequence homology allows the definition of rhodopsin, secretin, adhesion, glutamate and Frizzled receptor families. NC-IUPHAR recognizes Classes A, B, and C, which equate to the rhodopsin, secretin, and glutamate receptor families. The nomenclature of 7TM receptors is commonly used interchangeably with G protein-coupled receptors (GPCR), although the former nomenclature recognises signalling of 7TM receptors through pathways not involving G proteins. For example, adiponectin and membrane progestin receptors have some sequence homology to 7TM receptors but signal independently of G proteins and appear to reside in membranes in an inverted fashion compared to conventional GPCR. Additionally, the NPR-C natriuretic peptide receptor (see Page S195) has a single transmembrane domain structure, but appears to couple to G proteins to generate cellular responses. The 300+ non-olfactory GPCR are the targets for the majority of drugs in clinical usage (Overington et al., 2006), although only a minority of these receptors are exploited therapeutically.
  • Supplementary Table S4. FGA Co-Expressed Gene List in LUAD

    Supplementary Table S4. FGA Co-Expressed Gene List in LUAD

    Supplementary Table S4. FGA co-expressed gene list in LUAD tumors Symbol R Locus Description FGG 0.919 4q28 fibrinogen gamma chain FGL1 0.635 8p22 fibrinogen-like 1 SLC7A2 0.536 8p22 solute carrier family 7 (cationic amino acid transporter, y+ system), member 2 DUSP4 0.521 8p12-p11 dual specificity phosphatase 4 HAL 0.51 12q22-q24.1histidine ammonia-lyase PDE4D 0.499 5q12 phosphodiesterase 4D, cAMP-specific FURIN 0.497 15q26.1 furin (paired basic amino acid cleaving enzyme) CPS1 0.49 2q35 carbamoyl-phosphate synthase 1, mitochondrial TESC 0.478 12q24.22 tescalcin INHA 0.465 2q35 inhibin, alpha S100P 0.461 4p16 S100 calcium binding protein P VPS37A 0.447 8p22 vacuolar protein sorting 37 homolog A (S. cerevisiae) SLC16A14 0.447 2q36.3 solute carrier family 16, member 14 PPARGC1A 0.443 4p15.1 peroxisome proliferator-activated receptor gamma, coactivator 1 alpha SIK1 0.435 21q22.3 salt-inducible kinase 1 IRS2 0.434 13q34 insulin receptor substrate 2 RND1 0.433 12q12 Rho family GTPase 1 HGD 0.433 3q13.33 homogentisate 1,2-dioxygenase PTP4A1 0.432 6q12 protein tyrosine phosphatase type IVA, member 1 C8orf4 0.428 8p11.2 chromosome 8 open reading frame 4 DDC 0.427 7p12.2 dopa decarboxylase (aromatic L-amino acid decarboxylase) TACC2 0.427 10q26 transforming, acidic coiled-coil containing protein 2 MUC13 0.422 3q21.2 mucin 13, cell surface associated C5 0.412 9q33-q34 complement component 5 NR4A2 0.412 2q22-q23 nuclear receptor subfamily 4, group A, member 2 EYS 0.411 6q12 eyes shut homolog (Drosophila) GPX2 0.406 14q24.1 glutathione peroxidase