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Supplementary Table I Genes Regulated by Myc/Ras Transformation

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Supplementary Table I Genes regulated by myc/ras transformation signal Probe set Gene symbol gene + dox/ - E2 - dox/ - E2 - dox/ +E2 100011_at Klf3 Kruppel-like factor 3 (basic) 308 120 270 100013_at 2010008K16Rik RIKEN cDNA 2010008K16 gene 127 215 859 100016_at Mmp11 matrix metalloproteinase 11 187 71 150 100019_at Cspg2 chondroitin sulfate proteoglycan 2 1148 342 669 100023_at Mybl2 myeloblastosis oncogene-like 2 13 105 12 100030_at Upp uridine phosphorylase 18 39 110 100033_at Msh2 mutS homolog 2 (E. coli) 120 246 92 100037_at 2310005B10Rik RIKEN cDNA 2310005B10 gene 178 351 188 100039_at Tmem4 transmembrane protein 4 316 135 274 100040_at Mrpl17 mitochondrial ribosomal protein L17 88 142 89 100041_at 3010027G13Rik RIKEN cDNA 3010027G13 gene 818 1430 1033 methylenetetrahydrofolate dehydrogenase, methenyltetrahydrofolate 100046_at Mthfd2 cyclohydrolase 213 720 376 100064_f_at Gja1 gap junction membrane channel protein alpha 1 143 574 92 100066_at Gart phosphoribosylglycinamide formyltransferase 133 385 180 100071_at Mup2 major urinary protein 2 26 74 30 100081_at Stip1 stress-induced phosphoprotein 1 148 341 163 100089_at Ppic peptidylprolyl isomerase C 358 214 181 100091_at Ugalt2 UDP-galactose translocator 2 1456 896 1530 100095_at Scarb1 scavenger receptor class B, member 1 638 1044 570 100113_s_at Kifap3 kinesin-associated protein 3 482 168 311 100116_at 2810417H13Rik RIKEN cDNA 2810417H13 gene 134 261 53 100120_at Nid1 nidogen 1 81 47 54 100125_at Pa2g4 proliferation-associated 2G4, 38kD 62 286 44 100128_at Cdc2a cell division cycle 2 homolog A (S. pombe) 459 1382 247 100133_at Fyn Fyn proto-oncogene 168 44 82 100144_at Ncl nucleolin 1283 3452 1215 100151_at Tde1 tumor differentially expressed 1 620 351 620 100153_at Ncam1 neural cell adhesion molecule 1 302 144 234 100155_at Ddr1 discoidin domain receptor family, member 1 304 117 310 100156_at Mcmd5 mini chromosome maintenance deficient 5 (S. cerevisiae) 347 717 153 100272_at Smcy selected mouse cDNA on the Y 11 21 45 100279_at Siat5 sialyltransferase 5 125 75 76 100286_at Mst1 macrophage stimulating 1 (hepatocyte growth factor-like) 51 18 17 100290_f_at 6230416J20Rik RIKEN cDNA 6230416J20 gene 52 96 31 100291_at Cbl Casitas B-lineage lymphoma 31 56 43 100297_at 1600024A01Rik RIKEN cDNA 1600024A01 gene 120 73 90 100302_at Maff v-maf musculoaponeurotic fibrosarcoma oncogene family, protein F (avian) 21 53 26 100308_at Col8a1 procollagen, type VIII, alpha 1 931 262 949 100309_at Met met proto-oncogene 76 21 35 100342_i_at Tuba1 tubulin, alpha 1 5791 1931 4214 100353_g_at Hspa4 heat shock protein 4 435 703 466 100371_at Hnrpa1 heterogeneous nuclear ribonucleoprotein A1 31 64 28 100380_at H3f3a H3 histone, family 3A 1121 654 756 100412_g_at Aebp1 AE binding protein 1 2071 898 1427 100420_at Flg filaggrin 44 15 25 100429_at Ppox protoporphyrinogen oxidase 112 59 112 100435_at Edg2 endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 2 847 309 391 100453_at Camk2b calcium/calmodulin-dependent protein kinase II, beta 5 44 24 100465_i_at --- Mus musculus, clone IMAGE:3371572, mRNA 280 161 143 100482_at --- Mus musculus, clone IMAGE:5355325, mRNA 259 450 366 100483_at Ifnar1 interferon (alpha and beta) receptor 1 108 30 79 100486_at Ezh1 enhancer of zeste homolog 1 (Drosophila) 70 31 90 100488_at Gba acid beta glucosidase 659 309 845 100512_at Uchl5 ubiquitin carboxyl-terminal esterase L5 30 93 26 100539_at Bach-pending brain acyl-CoA hydrolase 208 353 201 100547_at 4921506I22Rik RIKEN cDNA 4921506I22 gene 237 99 99 100553_at Trim27 tripartite motif protein 27 226 606 230 100554_at Pdlim1 PDZ and LIM domain 1 (elfin) 72 221 188 100562_at Rangnrf-pending RAN guanine nucleotide release factor 107 280 73 100565_at Gnpi glucosamine-6-phosphate deaminase 140 67 101 100573_f_at Gpi1 glucose phosphate isomerase 1 191 329 221 100575_at Ard1 N-acetyltransferase ARD1 homolog (S. cerevisiae) 82 228 82 100577_at Snrpd1 small nuclear ribonucleoprotein D1 40 65 41 100578_at Impdh2 inosine 5'-phosphate dehydrogenase 2 502 1415 371 100580_at Clta clathrin, light polypeptide (Lca) 23 49 62 100593_at Tnnt2 troponin T2, cardiac 14 53 21 100596_at Selenbp1 selenium binding protein 1 8 53 36 100600_at Cd24a CD24a antigen 122 35 42 100603_at Dncic2 dynein, cytoplasmic, intermediate chain 2 118 56 89 100606_at Prnp prion protein 2702 1282 2648 100607_at Pld3 phospholipase D3 293 101 285 100636_at Eif4ebp1 eukaryotic translation initiation factor 4E binding protein 1 95 225 161 100697_at Pax3 paired box gene 3 11 21 11 100756_r_at Tyms-ps thymidylate synthase, pseudogene 86 214 148 100828_at Myla myosin light chain, alkali, cardiac atria 49 19 49 100877_at 1810058I24Rik RIKEN cDNA 1810058I24 gene 1074 585 744 100885_at Nek2 NIMA (never in mitosis gene a)-related expressed kinase 2 114 303 108 100886_f_at Mrpl45 mitochondrial ribosomal protein L45 154 296 180 100887_at 2810489L22Rik RIKEN cDNA 2810489L22 gene 44 80 41 100890_at 2600017H24Rik RIKEN cDNA 2600017H24 gene 90 214 106 100906_at Itgb7 integrin beta 7 178 468 627 100915_at Myh9 myosin heavy chain IX 2523 1461 2139 100923_at Myo10 myosin X 1122 293 776 100928_at Fbln2 fibulin 2 2508 1269 1442 100931_at Arsa arylsulfatase A 504 236 409 100953_at Timeless timeless homolog (Drosophila) 89 169 87 100955_at 2700084L22Rik RIKEN cDNA 2700084L22 gene 22 59 13 100974_at 1210002E11Rik RIKEN cDNA 1210002E11 gene 131 231 129 100977_at D530020C15Rik RIKEN cDNA D530020C15 gene 118 222 137 100983_at Prep prolyl endopeptidase 101 214 114 100986_at Fhl2 four and a half LIM domains 2 669 329 491 100988_at Bcl2l11 BCL2-like 11 (apoptosis facilitator) 321 164 211 100992_at Edr1 early development regulator 1 (homolog of polyhomeotic 1) 113 66 79 101015_s_at Ifnar2 interferon (alpha and beta) receptor 2 47 22 64 101027_s_at Pttg1 pituitary tumor-transforming 1 277 635 195 101039_at Col4a2 procollagen, type IV, alpha 2 1474 775 1095 101051_at S100a3 S100 calcium binding protein A3 66 109 80 101055_at Ppgb protective protein for beta-galactosidase 2084 1118 1996 101059_at Ndn necdin 336 171 193 101065_at Pcna proliferating cell nuclear antigen 291 826 204 101070_at Mkrn1 makorin, ring finger protein, 1 104 64 81 101073_at Lrp1 low density lipoprotein receptor-related protein 1 2161 979 2043 101083_s_at D17H6S56E-2 DNA segment, Chr 17, human D6S56E 2 266 578 183 101086_f_at Cnbp cellular nucleic acid binding protein 869 1657 882 101093_at Col4a1 procollagen, type IV, alpha 1 1164 552 787 101094_at Hig1-pending hypoxia induced gene 1 33 91 53 101099_at Nsg1 neuron specific gene family member 1 91 27 32 101105_at Bcrp1-pending breakpoint cluster region protein 1 1018 2228 1276 101108_at Nasp nuclear autoantigenic sperm protein (histone-binding) 41 73 34 101123_at Itm2b integral membrane protein 2B 1707 741 2165 101130_at Col1a2 procollagen, type I, alpha 2 7639 4621 8498 101180_at Atm ataxia telangiectasia mutated homolog (human) 87 176 194 101214_f_at Gapd glyceraldehyde-3-phosphate dehydrogenase 2161 3891 2701 101254_at Ran RAN, member RAS oncogene family 3763 6742 3389 101341_at H2-M9 histocompatibility 2, M region locus 9 21 44 50 101356_at Tk2 thymidine kinase 2, mitochondrial 102 56 76 101367_at Dctn1 dynactin 1 525 313 428 101384_at 2210008A03Rik RIKEN cDNA 2210008A03 gene 49 15 16 101385_at Mbd3 methyl-CpG binding domain protein 3 586 1060 533 101407_at Frda Friedreich ataxia 42 93 58 101414_at Lmnb2 lamin B2 67 118 52 101429_at Ddit3 DNA-damage inducible transcript 3 213 111 501 101433_at H2ls histocompatibility-2 complex class 1-like sequence 83 32 66 101435_at Akap2 A kinase (PRKA) anchor protein 2 96 41 68 101450_at Csf1 colony stimulating factor 1 (macrophage) 1316 609 1499 101451_at Peg3 paternally expressed 3 208 72 88 101453_at Mia melanoma inhibitory activity 18 35 29 101455_at Umps uridine monophosphate synthetase 40 91 16 101457_at Jak2 Janus kinase 2 54 30 66 101465_at Stat1 signal transducer and activator of transcription 1 103 57 679 101472_s_at Pklr pyruvate kinase liver and red blood cell 10 42 12 101484_at Nbr1 next to the Brca1 830 466 782 101485_at 2400003O03Rik RIKEN cDNA 2400003O03 gene 757 1231 722 101486_at Psmb10 proteasome (prosome, macropain) subunit, beta type 10 187 611 1047 101487_f_at Ly6e lymphocyte antigen 6 complex, locus E 3872 6614 10091 101489_at Amd1 S-adenosylmethionine decarboxylase 1 482 812 413 101494_at Afp alpha fetoprotein 19 45 40 101503_at Dpysl3 dihydropyrimidinase-like 3 119 55 61 101507_at 3110001I17Rik RIKEN cDNA 3110001I17 gene 31 7 43 101509_at Vbp1 von Hippel-Lindau binding protein 1 374 648 307 101515_at Acox1 acyl-Coenzyme A oxidase 1, palmitoyl 114 60 108 101516_at Cd59a CD59a antigen 88 31 88 101521_at Birc5 baculoviral IAP repeat-containing 5 89 232 55 101527_at Tcea1 transcription elongation factor A (SII) 1 509 829 521 101551_s_at Tes testis derived transcript 225 129 224 101554_at Nfkbia nuclear factor of kappa light chain gene enhancer in B-cells inhibitor, alpha 401 257 249 101560_at Emb embigin 2077 437 732 101576_f_at Spi1-2 serine protease inhibitor 1-2 80 43 68 101588_at Slc16a1 solute carrier family 16 (monocarboxylic acid transporters), member 1 28 64 34 101590_at Lamp2 lysosomal membrane glycoprotein 2 1238 506 1222 101623_at Slc16a8 solute carrier family 16 (monocarboxylic acid transporters), member 8 19 53 35 101624_at Kcns1 K+ voltage-gated channel, subfamily S, 1 38 22 39 101632_at Tnfrsf11a tumor necrosis factor receptor superfamily, member 11a 42 14 64 101634_at Npm1 nucleophosmin 1 2077 3442 1622 101650_at Pcdha6 protocadherin alpha 6 83 20 52 101764_at
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  • Research Article Characterization of the Equine Skeletal Muscle

    Research Article Characterization of the Equine Skeletal Muscle

    McGivney et al. BMC Genomics 2010, 11:398 http://www.biomedcentral.com/1471-2164/11/398 RESEARCH ARTICLE Open Access CharacterizationResearch article of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training Beatrice A McGivney1, Paul A McGettigan1, John A Browne1, Alexander CO Evans1,3, Rita G Fonseca2, Brendan J Loftus3, Amanda Lohan3, David E MacHugh1,3, Barbara A Murphy1, Lisa M Katz2 and Emmeline W Hill*1 Abstract Background: Digital gene expression profiling was used to characterize the assembly of genes expressed in equine skeletal muscle and to identify the subset of genes that were differentially expressed following a ten-month period of exercise training. The study cohort comprised seven Thoroughbred racehorses from a single training yard. Skeletal muscle biopsies were collected at rest from the gluteus medius at two time points: T1 - untrained, (9 ± 0.5 months old) and T2 - trained (20 ± 0.7 months old). Results: The most abundant mRNA transcripts in the muscle transcriptome were those involved in muscle contraction, aerobic respiration and mitochondrial function. A previously unreported over-representation of genes related to RNA processing, the stress response and proteolysis was observed. Following training 92 tags were differentially expressed of which 74 were annotated. Sixteen genes showed increased expression, including the mitochondrial genes ACADVL, MRPS21 and SLC25A29 encoded by the nuclear genome. Among the 58 genes with decreased expression, MSTN, a negative regulator of muscle growth, had the greatest decrease. Functional analysis of all expressed genes using FatiScan revealed an asymmetric distribution of 482 Gene Ontology (GO) groups and 18 KEGG pathways.
  • Supplementary Materials

    Supplementary Materials

    Supplementary Materials COMPARATIVE ANALYSIS OF THE TRANSCRIPTOME, PROTEOME AND miRNA PROFILE OF KUPFFER CELLS AND MONOCYTES Andrey Elchaninov1,3*, Anastasiya Lokhonina1,3, Maria Nikitina2, Polina Vishnyakova1,3, Andrey Makarov1, Irina Arutyunyan1, Anastasiya Poltavets1, Evgeniya Kananykhina2, Sergey Kovalchuk4, Evgeny Karpulevich5,6, Galina Bolshakova2, Gennady Sukhikh1, Timur Fatkhudinov2,3 1 Laboratory of Regenerative Medicine, National Medical Research Center for Obstetrics, Gynecology and Perinatology Named after Academician V.I. Kulakov of Ministry of Healthcare of Russian Federation, Moscow, Russia 2 Laboratory of Growth and Development, Scientific Research Institute of Human Morphology, Moscow, Russia 3 Histology Department, Medical Institute, Peoples' Friendship University of Russia, Moscow, Russia 4 Laboratory of Bioinformatic methods for Combinatorial Chemistry and Biology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia 5 Information Systems Department, Ivannikov Institute for System Programming of the Russian Academy of Sciences, Moscow, Russia 6 Genome Engineering Laboratory, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia Figure S1. Flow cytometry analysis of unsorted blood sample. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S2. Flow cytometry analysis of unsorted liver stromal cells. Representative forward, side scattering and histogram are shown. The proportions of negative cells were determined in relation to the isotype controls. The percentages of positive cells are indicated. The blue curve corresponds to the isotype control. Figure S3. MiRNAs expression analysis in monocytes and Kupffer cells. Full-length of heatmaps are presented.