Survey
* Your assessment is very important for improving the work of artificial intelligence, which forms the content of this project
Download Table S1
Document related concepts
no text concepts found
Transcript
Table S1. Gene expression analysis in 3D versus 2D A549 cell cultures. a Common name Affymetrix-ID Genbank Genes upregulated in 3D versus 2D FCGBP 203240_at NM_003890 MUC5AC 214303_x_at AW192795 MUC5AC 214385_s_at AI521646 MUC5B 213432_at AI697108 FGA 205649_s_at NM_000508 FGA 205650_s_at NM_021871 TXNIP 201010_s_at NM_006472 HAL 206643_at NM_002108 CHGB 204260_at NM_001819 TF 214063_s_at AI073407 TF 203400_s_at NM_001063 AGTR1 205357_s_at NM_000685 AGTR1 208016_s_at NM_004835 ADH6 214261_s_at H71135 CP 204846_at NM_000096 CP 227253_at AI922198 CP 1558034_s_at AL556703 CP 228143_at AI684991 SERPINA1 202833_s_at NM_000295 Description Fold change Signal log ratio Fc fragment of IgG binding protein mucin 5AC, oligomeric mucus/gel-forming mucin 5AC, oligomeric mucus/gel-forming mucin 5B, oligomeric mucus/gel-forming fibrinogen alpha chain fibrinogen alpha chain thioredoxin interacting protein histidine ammonia-lyase chromogranin B (secretogranin 1) transferrin transferrin angiotensin II receptor, type 1 angiotensin II receptor, type 1 alcohol dehydrogenase 6 (class V) ceruloplasmin (ferroxidase) ceruloplasmin (ferroxidase) ceruloplasmin (ferroxidase) ceruloplasmin (ferroxidase) serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 13.59 13.13 12.27 11.13 10.00 6.87 9.87 9.22 8.87 8.51 7.20 8.35 7.07 8.33 8.01 6.56 6.31 5.67 7.96 3.77 3.69 3.62 3.46 3.31 2.77 3.35 3.21 3.15 3.10 2.86 3.06 2.83 3.04 3.01 2.72 2.64 2.51 3.00 SERPINA1 211429_s_at AF119873 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 6.88 2.79 C13orf15 FGG AGR2 AGR2 AGR3 FLJ31568 FOSB KLF2 CYP3A5 CYP3A5 CYP3A5 HLA-DMB CEACAM1 218723_s_at 219612_s_at 228969_at 209173_at 228241_at 222274_at 202768_at 219371_s_at 214235_at 205765_at 214234_s_at 203932_at 209498_at NM_014059 NM_000509 AI922323 AF088867 AI827789 AW975050 NM_006732 NM_016270 X90579 NM_000777 X90579 NM_002118 X16354 7.95 7.95 7.54 2.42 7.41 7.30 7.17 6.78 6.63 5.99 5.99 6.34 6.33 2.99 2.99 2.91 1.27 2.89 2.76 2.82 2.75 2.71 2.57 2.56 2.67 2.67 C9orf152 CCL20 FGB FGB TFF1 KIAA1984 C4BPA TSPAN8 AHSG TTLL6 ATF3 CFB DUSP6 DUSP6 DUSP6 LOC91461 KRT4 ARRDC4 SERPINA6 229964_at 205476_at 204988_at 216238_s_at 205009_at 236518_at 205654_at 203824_at 210929_s_at 230924_at 202672_s_at 202357_s_at 208891_at 208892_s_at 208893_s_at 225380_at 213240_s_at 225283_at 206325_at AI380443 NM_004591 NM_005141 BG545288 NM_003225 BE208843 NM_000715 NM_004616 AF130057 AI698574 NM_001674 NM_001710 BC003143 BC003143 BC005047 BF528878 X07695 AV701177 NM_001756 chromosome 13 open reading frame 15 fibrinogen gamma chain anterior gradient homolog 2 (Xenopus laevis) anterior gradient homolog 2 (Xenopus laevis) anterior gradient homolog 3 (Xenopus laevis) FLJ31568 protein FBJ murine osteosarcoma viral oncogene homolog B Kruppel-like factor 2 (lung) cytochrome P450, family 3, subfamily A, polypeptide 5 cytochrome P450, family 3, subfamily A, polypeptide 5 cytochrome P450, family 3, subfamily A, polypeptide 5 major histocompatibility complex, class II, DM beta carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein) chromosome 9 open reading frame 152 chemokine (C-C motif) ligand 20 fibrinogen beta chain fibrinogen beta chain trefoil factor 1 KIAA1984 complement component 4 binding protein, alpha tetraspanin 8 alpha-2-HS-glycoprotein tubulin tyrosine ligase-like family, member 6 activating transcription factor 3 complement factor B dual specificity phosphatase 6 dual specificity phosphatase 6 dual specificity phosphatase 6 hypothetical protein BC007901 keratin 4 arrestin domain containing 4 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 6 6.28 6.26 6.19 5.94 6.11 6.08 5.96 5.96 5.87 5.74 5.72 5.51 5.46 5.13 4.43 5.36 5.26 5.13 5.10 2.66 2.64 2.63 2.56 2.61 2.59 2.58 2.56 2.55 2.52 2.51 2.46 2.45 2.36 2.14 2.42 2.39 2.39 2.34 SEPP1 ANXA13 APOH KLF4 KLF4 ST6GALNAC1 201427_s_at 208323_s_at 205216_s_at 221841_s_at 220266_s_at 227725_at NM_005410 NM_004306 NM_000042 BF514079 NM_004235 Y11339 selenoprotein P, plasma, 1 annexin A13 apolipoprotein H (beta-2-glycoprotein I) Kruppel-like factor 4 (gut) Kruppel-like factor 4 (gut) ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)N-acetylgalactosaminide alpha-2,6-sialyltransferase 1 5.08 4.99 4.97 4.93 3.46 4.77 2.34 2.32 2.31 2.29 1.79 2.26 TFPI 210665_at AF021834 tissue factor pathway inhibitor (lipoprotein-associated 4.76 2.25 Table S1. Gene expression analysis in 3D versus 2D A549 cell cultures. a Common name Affymetrix-ID Genbank TFPI 214378_at BF109662 TFPI 209676_at J03225 TFPI 210664_s_at AF021834 TFPI 213258_at BF511231 NR4A2 NR4A2 NR4A2 NR4A3 ERBB3 216248_s_at 204622_x_at 204621_s_at 216979_at 202454_s_at S77154 NM_006186 AI935096 X89894 NM_001982 ERBB3 226213_at AV681807 ORM1/ORM2 TMEM178 CDH17 FMO5 MAFF 205041_s_at 229302_at 209847_at 205776_at 36711_at NM_000607 AA058832 U07969 NM_001461 AL021977 DDC 205311_at NM_000790 LOC653879 PLXNC1 RP5-1022P6.2 RP5-1022P6.2 RP5-1022P6.2 CORO2A CORO2A TNFSF10 TNFSF10 TNFSF10 FLJ32252 DKFZP564O0823 SLPI IFITM1 IFITM1 MALAT1 217767_at 213241_at 224835_at 224826_at 230492_s_at 227177_at 205538_at 202688_at 202687_s_at 214329_x_at 1557146_a_at 225809_at 203021_at 214022_s_at 201601_x_at 224558_s_at NM_000064 AF035307 AL109935 AK001947 BE328402 AL515381 NM_003389 NM_003810 U57059 AW474434 T03074 AI659927 NM_003064 AA749101 NM_003641 AI446756 GBA3 AQP3 PLEKHH2 222943_at 39248_at 227148_at AW235567 N74607 AI913749 FGL1 CPB2 HNMT NEB ABCA8 ENTPD2 USH1C USH1C HLA-DMA ITIH2 PDZK1 CITED2 205305_at 206651_s_at 204112_s_at 205054_at 204719_at 230430_at 211184_s_at 205137_x_at 217478_s_at 204987_at 205380_at 207980_s_at NM_004467 NM_016413 NM_006895 NM_004543 NM_007168 AW134837 AB006955 NM_005709 X76775 NM_002216 NM_002614 NM_006079 CITED2 209357_at AF109161 LOC648556 GSTA1 ASGR1 PSCDBP 232696_at 203924_at 206743_s_at 209606_at AI394334 NM_000846 NM_001671 L06633 TMF1 TOX3 242243_at 214774_x_at AI767435 AK027006 Description Fold change Signal log ratio 4.60 2.21 4.25 2.09 3.24 1.70 2.82 1.50 4.70 4.52 4.18 4.64 4.64 2.22 2.17 2.06 2.21 2.21 4.54 2.18 4.62 4.62 4.59 4.53 4.49 2.20 2.19 2.20 2.18 2.16 4.44 2.15 4.43 4.36 4.29 3.50 2.98 4.28 3.72 4.27 3.65 3.54 4.27 4.26 4.26 4.19 3.61 4.15 2.15 2.13 2.10 1.81 1.58 2.10 1.90 2.10 1.87 1.84 2.09 2.09 2.09 2.06 1.85 2.04 4.12 4.12 4.07 2.04 2.04 2.02 4.07 3.96 3.93 3.90 3.87 3.87 3.86 3.19 3.84 3.83 3.83 3.83 2.02 1.98 1.99 1.98 1.96 1.94 1.95 1.67 1.94 1.94 1.93 1.94 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2 3.55 1.83 uncharacterized gastric protein ZA43P glutathione S-transferase A1 asialoglycoprotein receptor 1 pleckstrin homology, Sec7 and coiled-coil domains, binding protein TATA element modulatory factor 1 TOX high mobility group box family member 3 3.80 3.80 3.79 3.68 1.93 1.93 1.92 1.87 3.67 3.67 1.87 1.87 coagulation inhibitor) tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) nuclear receptor subfamily 4, group A, member 2 nuclear receptor subfamily 4, group A, member 2 nuclear receptor subfamily 4, group A, member 2 nuclear receptor subfamily 4, group A, member 3 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) orosomucoid 1///orosomucoid 2 transmembrane protein 178 cadherin 17, LI cadherin (liver-intestine) flavin containing monooxygenase 5 v-maf musculoaponeurotic fibrosarcoma oncogene homolog F (avian) dopa decarboxylase (aromatic L-amino acid decarboxylase) similar to Complement C3 precursor plexin C1 hypothetical protein KIAA1434 hypothetical protein KIAA1434 hypothetical protein KIAA1434 coronin, actin binding protein, 2A coronin, actin binding protein, 2A tumor necrosis factor (ligand) superfamily, member 10 tumor necrosis factor (ligand) superfamily, member 10 tumor necrosis factor (ligand) superfamily, member 10 hypothetical protein FLJ32252 DKFZP564O0823 protein secretory leukocyte peptidase inhibitor interferon induced transmembrane protein 1 (9-27) interferon induced transmembrane protein 1 (9-27) metastasis associated lung adenocarcinoma transcript 1 (non-coding RNA) glucosidase, beta, acid 3 (cytosolic) aquaporin 3 (Gill blood group) pleckstrin homology domain containing, family H (with MyTH4 domain) member 2 fibrinogen-like 1 carboxypeptidase B2 (plasma) histamine N-methyltransferase nebulin ATP-binding cassette, sub-family A (ABC1), member 8 ectonucleoside triphosphate diphosphohydrolase 2 Usher syndrome 1C (autosomal recessive, severe) Usher syndrome 1C (autosomal recessive, severe) major histocompatibility complex, class II, DM alpha inter-alpha (globulin) inhibitor H2 PDZ domain containing 1 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2 Table S1. Gene expression analysis in 3D versus 2D A549 cell cultures. a Common name Affymetrix-ID Genbank Description Fold change 3.55 3.35 3.66 3.65 Signal log ratio 1.82 1.74 1.87 1.84 TOX3 TOX3 CFD SLC1A2 216623_x_at 215108_x_at 205382_s_at 225491_at AK025084 U80736 NM_001928 AL157452 IGFBP1 LOC145837 PDK4 PDK4 HAO1 CNTNAP3 LOC692247 ID2/ID2B 205302_at 239594_at 225207_at 1562321_at 220224_at 233202_at 1569453_a_at 213931_at NM_000596 BF110735 AV707102 AL832708 NM_017545 AI433163 BG772667 AI819238 SLC16A6 230748_at AI873273 PLA1A CFH C6orf86 EHF SLC4A4 219584_at 213800_at 242055_at 225645_at 203908_at NM_015900 X04697 AW136397 AI763378 NM_003759 TM4SF4 C12orf39 KCNJ2 209937_at 229778_at 206765_at BC001386 BE326710 AF153820 WNT4 SLC40A1 208606_s_at 223044_at NM_030761 AL136944 S100P MED31 SEMA4G 204351_at 236241_at 219194_at NM_005980 BF593977 NM_017893 VIL1 PDE4B 228912_at 215671_at AI436136 AU144792 TOX high mobility group box family member 3 TOX high mobility group box family member 3 complement factor D (adipsin) solute carrier family 1 (glial high affinity glutamate transporter), member 2 insulin-like growth factor binding protein 1 hypothetical protein LOC145837 pyruvate dehydrogenase kinase, isozyme 4 pyruvate dehydrogenase kinase, isozyme 4 hydroxyacid oxidase (glycolate oxidase) 1 contactin associated protein-like 3 hypothetical locus LOC692247 inhibitor of DNA binding 2, dominant negative helix-loophelix protein///inhibitor of DNA binding 2B, dominant negative helix-loop-helix protein solute carrier family 16, member 6 (monocarboxylic acid transporter 7) phospholipase A1 member A complement factor H Chromosome 6 open reading frame 86 Ets homologous factor solute carrier family 4, sodium bicarbonate cotransporter, member 4 transmembrane 4 L six family member 4 chromosome 12 open reading frame 39 potassium inwardly-rectifying channel, subfamily J, member 2 wingless-type MMTV integration site family, member 4 solute carrier family 40 (iron-regulated transporter), member 1 S100 calcium binding protein P mediator complex subunit 31 sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4G Villin 1 phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila) 3.63 3.63 3.63 2.62 3.62 3.62 3.53 3.53 1.85 1.86 1.86 1.39 1.86 1.86 1.82 1.80 3.51 1.83 3.50 3.48 3.47 3.44 3.43 1.81 1.80 1.80 1.79 1.76 3.41 3.38 3.37 1.77 1.77 1.77 3.37 3.36 1.75 1.75 3.33 3.33 3.33 1.74 1.73 1.73 3.33 3.29 1.73 1.72 LGALS4 PTGS2 204272_at NM_006149 lectin, galactoside-binding, soluble, 4 (galectin 4) 1554997_a_at AY151286 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) 3.28 3.25 1.72 1.70 PTGS2 204748_at NM_000963 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase) 3.04 1.61 IL8 HK2 FOS TM4SF5 FLJ37512 202859_x_at 202934_at 209189_at 206242_at 244065_at NM_000584 AI761561 BC004490 NM_003963 AW016751 interleukin 8 hexokinase 2 v-fos FBJ murine osteosarcoma viral oncogene homolog transmembrane 4 L six family member 5 similar to Contactin-associated protein-like 3 precursor (Cell recognition molecule Caspr3) 3.22 3.17 3.17 3.16 3.16 1.68 1.67 1.67 1.66 1.66 SLC23A1 223732_at AF170911 3.15 1.65 SELENBP1 HES1 PCSK6 PCSK6 CLDN2 FGFR3 214433_s_at 203394_s_at 242662_at 207414_s_at 223509_at 204379_s_at NM_003944 BE973687 AI056815 NM_002570 AF177340 NM_000142 3.07 3.07 3.06 2.82 3.06 3.05 1.62 1.61 1.61 1.50 1.60 1.60 C5 MYLIP FN1 FN1 FN1 FN1 CYP4F3 CPN1 SPRY1 205500_at 228097_at 212464_s_at 216442_x_at 210495_x_at 211719_x_at 206515_at 206256_at 212558_at NM_001735 AW292746 X02761 AK026737 AF130095 BC005858 NM_000896 NM_001308 BF508662 solute carrier family 23 (nucleobase transporters), member 1 selenium binding protein 1 hairy and enhancer of split 1, (Drosophila) Proprotein convertase subtilisin/kexin type 6 proprotein convertase subtilisin/kexin type 6 claudin 2 fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism) complement component 5 myosin regulatory light chain interacting protein fibronectin 1 fibronectin 1 fibronectin 1 fibronectin 1 cytochrome P450, family 4, subfamily F, polypeptide 3 carboxypeptidase N, polypeptide 1 sprouty homolog 1, antagonist of FGF signaling (Drosophila) 3.04 3.04 3.02 2.99 2.96 2.95 3.01 3.01 2.99 1.60 1.60 1.59 1.58 1.56 1.56 1.59 1.59 1.58 Table S1. Gene expression analysis in 3D versus 2D A549 cell cultures. a Common name Affymetrix-ID Genbank Description Fold change 2.98 2.95 2.95 2.93 2.91 2.90 2.90 2.90 2.88 Signal log ratio 1.57 1.57 1.56 1.56 1.53 1.54 1.54 1.53 1.52 RHOBTB1 CA9 TSC22D3 PLXNA2 IFITM2 XBP1 TM4SF20 TMED10 CEACAM6 212651_at 205199_at 208763_s_at 213030_s_at 201315_x_at 200670_at 220639_at 238886_at 203757_s_at AB018283 NM_001216 AL110191 AI688418 NM_006435 NM_005080 NM_024795 BF056141 BC005008 Rho-related BTB domain containing 1 carbonic anhydrase IX TSC22 domain family, member 3 plexin A2 interferon induced transmembrane protein 2 (1-8D) X-box binding protein 1 transmembrane 4 L six family member 20 Transmembrane emp24-like trafficking protein 10 (yeast) carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen) CEACAM6 211657_at M18728 carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen) 2.63 1.40 RARRES1 RARRES1 BACH1 221872_at 206392_s_at 204194_at AI669229 retinoic acid receptor responder (tazarotene induced) 1 NM_002888 retinoic acid receptor responder (tazarotene induced) 1 NM_001186 BTB and CNC homology 1, basic leucine zipper transcription factor 1 NM_002135 nuclear receptor subfamily 4, group A, member 1 AU155094 Annexin A1 AF260333 chromosome 4 open reading frame 18 AK002203 nitric oxide synthase trafficker AI479168 organic solute transporter beta BF195709 calpain 5 NM_014298 quinolinate phosphoribosyltransferase (nicotinatenucleotide pyrophosphorylase (carboxylating)) 2.87 2.63 2.84 1.52 1.39 1.51 NR4A1 ANXA1 C4orf18 NOSTRIN OSTbeta CAPN5 QPRT 202340_x_at 233011_at 223204_at 226992_at 230830_at 226292_at 204044_at 2.83 2.82 2.81 2.78 2.77 2.71 2.70 1.50 1.49 1.49 1.47 1.47 1.44 1.43 SLC44A5 LCN2 RPL31 PPP1R15A NFKBIZ 235763_at 212531_at 200962_at 202014_at 223218_s_at AA001450 NM_005564 AI348010 NM_014330 AB037925 2.70 2.67 2.67 2.67 2.66 1.43 1.42 1.42 1.41 1.42 ANK3 LOC284454 KLF6 F7 206385_s_at 1555847_a_at 1555832_s_at 207300_s_at NM_020987 BU617052 BU683415 NM_000131 2.66 2.62 2.62 2.61 1.41 1.39 1.39 1.39 MAOA CD302 RNASE4 LOC202134/LOC 653316/NY-REN7 PROS1 EEF1A1 TGFBR2 BCL6 MAP3K1 RNASE4 C5orf26 GPR37 212741_at 203799_at 205158_at 214945_at AA923354 NM_014880 NM_002937 AW514267 2.60 2.60 2.51 2.50 1.38 1.38 1.33 1.32 207808_s_at 227708_at 208944_at 203140_at 225927_at 213397_x_at 225698_at 214586_at NM_000313 AW469790 D50683 NM_001706 AA541479 AI761728 BF314746 T16257 2.46 2.45 2.43 2.36 2.35 2.34 2.34 2.33 1.30 1.29 1.28 1.24 1.23 1.23 1.23 1.22 SLC23A2 209236_at 2.30 1.20 ST6GAL1 ANG 201998_at 205141_at 2.27 2.25 1.18 1.17 -13.20 -12.68 -3.76 -3.66 -11.43 -3.52 -12.43 -3.64 -10.55 -9.93 -7.50 -10.10 -10.05 -3.41 -3.32 -2.91 -3.34 -3.33 solute carrier family 44, member 5 lipocalin 2 (oncogene 24p3) ribosomal protein L31 protein phosphatase 1, regulatory (inhibitor) subunit 15A nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta ankyrin 3, node of Ranvier (ankyrin G) hypothetical protein LOC284454 Kruppel-like factor 6 coagulation factor VII (serum prothrombin conversion accelerator) monoamine oxidase A CD302 molecule ribonuclease, RNase A family, 4 NY-REN-7 antigen///hypothetical protein LOC202134///hypothetical protein LOC653316 protein S (alpha) eukaryotic translation elongation factor 1 alpha 1 transforming growth factor, beta receptor II (70/80kDa) B-cell CLL/lymphoma 6 (zinc finger protein 51) mitogen-activated protein kinase kinase kinase 1 ribonuclease, RNase A family, 4 chromosome 5 open reading frame 26 G protein-coupled receptor 37 (endothelin receptor type B-like) AL389886 solute carrier family 23 (nucleobase transporters), member 2 AI743792 ST6 beta-galactosamide alpha-2,6-sialyltranferase 1 NM_001145 angiogenin, ribonuclease, RNase A family, 5 Genes downregulated in 3D versus 2D BCL2A1 205681_at NM_004049 BCL2-related protein A1 GREM1 218468_s_at AF154054 gremlin 1, cysteine knot superfamily, homolog (Xenopus laevis) GREM1 218469_at NM_013372 gremlin 1, cysteine knot superfamily, homolog (Xenopus laevis) SPOCK1 202363_at AF231124 sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1 TMEPAI 222450_at AL035541 transmembrane, prostate androgen induced RNA TMEPAI 222449_at AL035541 transmembrane, prostate androgen induced RNA TMEPAI 217875_s_at NM_020182 transmembrane, prostate androgen induced RNA HAS2 206432_at NM_005328 hyaluronan synthase 2 MYOCD 237206_at AI452798 myocardin Table S1. Gene expression analysis in 3D versus 2D A549 cell cultures. a Common name Affymetrix-ID Genbank Description LBH COL5A1 COL5A1 COL5A1 CDH4 NPTX1 PLAU PLAU GLIPR1 GLIPR1 GLIPR1 TNFAIP6 TNFAIP6 DIRAS3 ITGB6 IL11 DIO2 DIO2 NPR3 221011_s_at 203325_s_at 212488_at 212489_at 220227_at 204684_at 211668_s_at 205479_s_at 226136_at 226142_at 204222_s_at 206026_s_at 206025_s_at 215506_s_at 226535_at 206924_at 203700_s_at 203699_s_at 219790_s_at NM_030915 AI130969 N30339 AI983428 NM_024883 NM_002522 K03226 NM_002658 N32834 AV682252 NM_006851 NM_007115 AW188198 AK021882 AK026736 NM_000641 NM_013989 U53506 NM_000908 limb bud and heart development homolog (mouse) collagen, type V, alpha 1 collagen, type V, alpha 1 collagen, type V, alpha 1 cadherin 4, type 1, R-cadherin (retinal) neuronal pentraxin I plasminogen activator, urokinase plasminogen activator, urokinase GLI pathogenesis-related 1 (glioma) GLI pathogenesis-related 1 (glioma) GLI pathogenesis-related 1 (glioma) tumor necrosis factor, alpha-induced protein 6 tumor necrosis factor, alpha-induced protein 6 DIRAS family, GTP-binding RAS-like 3 integrin, beta 6 interleukin 11 deiodinase, iodothyronine, type II deiodinase, iodothyronine, type II natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C) NPR3 219789_at AI628360 BCAT1 BCAT1 BCAT1 MOBKL2B MOBKL2B CXCR7 C15orf48 EDG3 214452_at 225285_at 226517_at 229568_at 226844_at 212977_at 223484_at 228176_at NM_005504 AK025615 AL390172 AI692878 AI375115 AI817041 AF228422 AA534817 AFAP1L2 RNF182 IGFBP7 IGFBP7 KRT80 ANXA10 TNFRSF12A RDX RDX KCNMA1 226829_at 230720_at 201162_at 201163_s_at 231849_at 210143_at 218368_s_at 204969_s_at 212398_at 221583_s_at AW138743 AI884906 NM_001553 NM_001553 AL162069 AF196478 NM_016639 NM_002906 AI057093 AI129381 KCNMA1 221584_s_at CCDC80 PAQR5 SPARC GNG2 FBN2 IGFBP6 FLRT2 OSAP LYPD1 P4HA3 225242_s_at 220333_at 200665_s_at 224964_s_at 203184_at 203851_at 204359_at 223734_at 212909_at 228703_at SOCS2 SLC7A11 203372_s_at 207528_s_at PLCE1 PGM2L1 NAV3 NAV3 DST MAF Fold change -8.88 -7.92 -6.15 -5.28 -7.79 -7.69 -7.35 -5.23 -7.10 -6.28 -5.81 -6.87 -5.28 -6.84 -6.78 -6.77 -6.41 -5.19 -5.70 Signal log ratio -3.15 -2.98 -2.62 -2.40 -2.98 -2.95 -2.94 -2.39 -2.84 -2.65 -2.55 -2.78 -2.33 -2.77 -2.77 -2.77 -2.74 -2.37 -2.49 natriuretic peptide receptor C/guanylate cyclase C (atrionatriuretic peptide receptor C) -4.30 -2.13 branched chain aminotransferase 1, cytosolic branched chain aminotransferase 1, cytosolic branched chain aminotransferase 1, cytosolic MOB1, Mps One Binder kinase activator-like 2B (yeast) MOB1, Mps One Binder kinase activator-like 2B (yeast) chemokine (C-X-C motif) receptor 7 chromosome 15 open reading frame 48 endothelial differentiation, sphingolipid G-protein-coupled receptor, 3 actin filament associated protein 1-like 2 ring finger protein 182 insulin-like growth factor binding protein 7 insulin-like growth factor binding protein 7 keratin 80 annexin A10 tumor necrosis factor receptor superfamily, member 12A radixin radixin potassium large conductance calcium-activated channel, subfamily M, alpha member 1 -5.29 -3.18 -3.07 -5.27 -3.64 -5.27 -5.19 -5.04 -2.40 -1.67 -1.63 -2.40 -1.87 -2.41 -2.40 -2.35 -4.94 -4.90 -4.73 -4.72 -4.52 -4.44 -4.43 -4.42 -3.36 -4.41 -2.33 -2.32 -2.24 -2.24 -2.19 -2.20 -2.18 -2.15 -1.75 -2.14 U11058 potassium large conductance calcium-activated channel, subfamily M, alpha member 1 -2.79 -1.48 AW303375 NM_017705 NM_003118 AK026424 NM_001999 NM_002178 NM_013231 AF329088 AL567376 AW665086 coiled-coil domain containing 80 progestin and adipoQ receptor family member V secreted protein, acidic, cysteine-rich (osteonectin) guanine nucleotide binding protein (G protein), gamma 2 fibrillin 2 (congenital contractural arachnodactyly) insulin-like growth factor binding protein 6 fibronectin leucine rich transmembrane protein 2 ovary-specific acidic protein LY6/PLAUR domain containing 1 procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide III -4.40 -4.37 -4.27 -4.24 -4.22 -4.08 -4.04 -4.02 -3.98 -3.96 -2.15 -2.14 -2.09 -2.11 -2.08 -2.03 -2.02 -2.02 -2.01 -1.99 -3.95 -3.79 -1.98 -1.93 -3.77 -3.74 -3.73 -3.34 -3.71 -3.70 -1.91 -1.91 -1.90 -1.73 -1.89 -1.89 AB004903 suppressor of cytokine signaling 2 NM_014331 solute carrier family 7, (cationic amino acid transporter, y+ system) member 11 205111_s_at NM_016341 phospholipase C, epsilon 1 229553_at AA736452 phosphoglucomutase 2-like 1 204823_at NM_014903 neuron navigator 3 1552658_a_at NM_014903 neuron navigator 3 204455_at NM_001723 dystonin 209348_s_at AF055376 v-maf musculoaponeurotic fibrosarcoma oncogene homolog (avian) Table S1. Gene expression analysis in 3D versus 2D A549 cell cultures. a a Common name Affymetrix-ID Genbank Description Fold change -3.68 Signal log ratio -1.89 SERPINE1 202628_s_at NM_000602 serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 LOXL2 SCD PLAT ADRB1 HERC5 SEPT6 SEPT6 PDXK NEXN NEXN NUPR1 FHL1 FHL1 FHL1 TIMP2 TIMP2 TIMP2 WDR1 APBB1IP 202998_s_at 211708_s_at 201860_s_at 229309_at 219863_at 1555526_a_at 212415_at 202671_s_at 1552309_a_at 226103_at 209230_s_at 214505_s_at 210299_s_at 201540_at 224560_at 203167_at 231579_s_at 210935_s_at 230925_at NM_002318 BC005807 NM_000930 AI625747 NM_016323 AF403061 AW150913 NM_003681 NM_144573 AF114264 AF135266 AF220153 AF063002 NM_001449 BF107565 NM_003255 BE968786 AF274954 AI093231 lysyl oxidase-like 2 stearoyl-CoA desaturase (delta-9-desaturase) plasminogen activator, tissue adrenergic, beta-1-, receptor hect domain and RLD 5 septin 6 septin 6 pyridoxal (pyridoxine, vitamin B6) kinase nexilin (F actin binding protein) nexilin (F actin binding protein) nuclear protein 1 four and a half LIM domains 1 four and a half LIM domains 1 four and a half LIM domains 1 TIMP metallopeptidase inhibitor 2 TIMP metallopeptidase inhibitor 2 TIMP metallopeptidase inhibitor 2 WD repeat domain 1 amyloid beta (A4) precursor protein-binding, family B, member 1 interacting protein -3.62 -3.59 -3.57 -3.54 -3.51 -3.51 -2.79 -3.46 -3.45 -3.30 -3.42 -3.41 -3.37 -2.84 -3.39 -2.92 -2.87 -3.38 -3.38 -1.86 -1.86 -1.84 -1.83 -1.81 -1.81 -1.48 -1.80 -1.79 -1.72 -1.78 -1.78 -1.76 -1.51 -1.76 -1.55 -1.52 -1.77 -1.76 AKAP2/PALM2AKAP2 ANKRD29 ITGA4 226694_at BG540494 A kinase (PRKA) anchor protein 2///PALM2-AKAP2 protein ankyrin repeat domain 29 integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA4 receptor) collagen, type IV, alpha 1 sterile alpha motif domain containing 9 neuropilin 2 neuropilin 2 kinesin family member 3C secretogranin II (chromogranin C) SKI-like oncogene heme oxygenase (decycling) 1 Protease, serine, 23 ADAM metallopeptidase domain 19 (meltrin beta) basonuclin 2 cell adhesion molecule 1 cell adhesion molecule 1 peptidyl arginine deiminase, type II EF-hand domain family, member B dermatan sulfate epimerase lipoma HMGIC fusion partner CDC42 effector protein (Rho GTPase binding) 3 CDC42 effector protein (Rho GTPase binding) 3 Similar to LOC166075 tropomyosin 1 (alpha) EPH receptor B2 chromosome 1 open reading frame 43 mitochondrial ribosomal protein S12 Niemann-Pick disease, type C1 microfibrillar-associated protein 3-like cytokine-like nuclear factor n-pac///septin 6 thrombomodulin R-spondin 3 homolog (Xenopus laevis) pleckstrin 2 neuron navigator 2 chromosome 8 open reading frame 13 transforming growth factor, beta-induced, 68kDa coactosin-like 1 (Dictyostelium) -3.37 -1.75 238332_at 213416_at AI307802 BG532690 -3.36 -3.25 -1.76 -1.71 COL4A1 SAMD9 NRP2 NRP2 KIF3C SCG2 SKIL HMOX1 PRSS23 ADAM19 BNC2 CADM1 CADM1 PADI2 EFHB DSE LHFP CDC42EP3 CDC42EP3 LOC401097 TPM1 EPHB2 C1orf43 MRPS12 NPC1 MFAP3L N-PAC/SEPT6 THBD RSPO3 PLEK2 NAV2 C8orf13 TGFBI COTL1 211981_at 228531_at 214632_at 211844_s_at 203390_s_at 204035_at 206675_s_at 203665_at 229441_at 209765_at 220272_at 209030_s_at 209031_at 209791_at 239477_at 218854_at 218656_s_at 209286_at 209288_s_at 236738_at 206116_s_at 211165_x_at 1555225_at 204330_s_at 202679_at 205442_at 212414_s_at 203888_at 228186_s_at 218644_at 218330_s_at 226614_s_at 201506_at 221059_s_at NM_001845 AA741307 AA295257 AF022859 NM_002254 NM_003469 NM_005414 NM_002133 AI569872 Y13786 NM_017637 NM_014333 AL519710 AL049569 BF941046 NM_013352 NM_005780 AI754416 AL136842 AW057589 NM_000366 D31661 BC008306 AA587905 NM_000271 NM_021647 D50918 NM_000361 BF589322 NM_016445 NM_018162 BE856336 NM_000358 NM_021615 -3.21 -3.20 -3.19 -3.06 -3.15 -3.13 -3.12 -3.12 -3.10 -3.02 -3.00 -2.94 -2.59 -2.92 -2.91 -2.83 -2.82 -2.77 -2.67 -2.74 -2.74 -2.72 -2.66 -2.64 -2.62 -2.62 -2.57 -2.57 -2.54 -2.47 -2.46 -2.45 -2.43 -2.35 -1.68 -1.68 -1.68 -1.62 -1.65 -1.65 -1.64 -1.64 -1.64 -1.60 -1.59 -1.55 -1.37 -1.54 -1.54 -1.50 -1.50 -1.47 -1.42 -1.46 -1.46 -1.45 -1.41 -1.40 -1.39 -1.39 -1.36 -1.36 -1.35 -1.30 -1.30 -1.29 -1.28 -1.23 Listing of up- and downregulated genes according to SAM.
Related documents