Table 1.

Down-regulation of gene expression by N-myc

Tag sequenceRatio *SHEP2 SHEP21N PUnigeneGeneDescription
Cytoskeleton
    GTTTCTAATA105.80.60.00631095MAP4Microtubule-associated protein 4
    TGCTACGAAA105.80.60.006146550MYH9Myosin, heavy polypeptide 9, nonmuscle
    TGCTAAAAAA535.17.50.000146550MYH9Myosin, heavy polypeptide 9, nonmuscle
    TTAAAGATTT926.52.90.000133892TPM1Tropomyosin 1 (α)
    ACAGGCTACG911.21.20.000410977TAGLNTransgelin
    TGTAGAAAAA78.51.20.001512712TUBBTubulin, β polypeptide
    TCCAAATCGA66.71.20.008435800VIMVimentin
    AAGAGGTTTG58.51.70.00474368CKAP4Cytoskeleton-associated protein 4
    GGTTAATTGA>4400.00714376ACTG1Actin, γ 1
    TAATATTTTT411.72.90.002443619ACTN4Actinin, α 4
    CCCTTAGCTT413.53.50.001233936MRCL3Myosin regulatory light chain MRCL3
    GCTTTATTTG331.99.90.000426930ACTBActin, β
    AACTGCTTCA225.610.50.001433506ARPC1BActin-related protein 2/3 complex, subunit 1B, 41 kDa
    TGTACCTGTA228.311.60.001446608K-ALPHA-1Tubulin, α, ubiquitous
    CTGCCAAGTT220.78.70.00475873ZYXZyxin
ECM structural
    ATCTTGTTAC2213.50.60.000418138FN1Fibronectin 1
    TGCAATATGC>1211.700.000750FBN1Fibrillin 1 (Marfan syndrome)
    TTAAATAGCA116.70.60.002172928COL1A1Collagen, type I, α 1
    TGGAAATGCC813.91.70.000172928COL1A1Collagen, type I, α 1
    TTCGGTTGGT520.24.10.000172928COL1A1Collagen, type I, α 1
    GGAGGAGAGC>54.900.003172928COL1A1Collagen, type I, α 1
    TGGAAATGAC585.915.70.000172928COL1A1Collagen, type I, α 1
    TGAAATTGTC>44.500.004172928COL1A1Collagen, type I, α 1
    ACCAAAAACC242.723.20.002172928COL1A1Collagen, type I, α 1
    GACCGCAGGA116.70.60.002437173COL4A1Collagen, type IV, α 1
    ACAGATTTGA>99.400.000114599COL8A1Collagen, type VIII, α 1
    TAAAAACAAA95.40.60.010114599COL8A1Collagen, type VIII, α 1
    TAATCCTCAA715.32.30.000413175COL18ACollagen, type XVIII, α 1
    TCTTGATATT>55.400.004283393COL5A2Collagen, type V, α 2
ECM regulator
    TTTGCACCTT5835.10.60.000410037CTGFConnective tissue growth factor
    ATGTGAAGAG22539250.000111779SPARCSecreted protein, acidic, cysteine-rich (osteonectin)
    AAAAAGCTGC>1514.800.000111779SPARCSecreted protein, acidic, cysteine-rich (osteonectin)
    GGTGGACACG>1212.100.000111779SPARCSecreted protein, acidic, cysteine-rich (osteonectin)
    CTAAAAACCT>99.400.000111779SPARCSecreted protein, acidic, cysteine-rich (osteonectin)
    TTAGTGTCGT89.91.20.000111779SPARCSecreted protein, acidic, cysteine-rich (osteonectin)
    TAAAAATGTT835.14.60.000119000PAI1Plasminogen activator inhibitor type 1
    TCTCTGATGC325.28.10.0006441TIMP2Tissue inhibitor of metalloproteinase 2
Extracellular
    CTTTCTTTGA>87.600.000130865DKK3DKK3 dickkopf homologue 3 (Xenopus laevis)
    GTTTTTTTTA610.31.70.001437656LEPRE1Leucine proline-enriched proteoglycan (leprecan) 1
    CATTATAACT137.60.60.00184359DULLARDDullard homologue (Xenopus laevis)
    AAGGAAATGA>44.500.004484063SLIT3Slit homologue 3 (Drosophila)
    CATATCATTA>1514.800.000435795IGFBP7Insulin-like growth factor binding protein 7
    GCCCCAATAA>1010.300.000407909LGALS1Lectin, galactoside-binding, soluble, 1 (galectin 1)
Signal transduction
    AAGCCTTGCT95.40.60.010411366GRB2Growth factor receptor-bound protein 2
    TCCGTGGTTG>87.600.000511745BASP1Brain abundant, membrane attached signal protein 1
    TCTCAATTCT412.62.90.001146409CDC42Cell division cycle 42 (GTP binding protein, 25 kDa)
    TCCTGTAAAG414.44.10.00174034CAV1Caveolin 1, caveolae protein, 22 kDa
    AGCAGATCAG226.5110.001143873S100A10S100 calcium binding protein A10 (annexin II ligand, calpactin I, light polypeptide (p11))
Integral to membrane
    TGGCCTAATA4325.60.60.0001501SDC2Syndecan 2 (heparan sulfate proteoglycan 1)
    TGGCCTAAAA>44.500.0041501SDC2Syndecan 2 (heparan sulfate proteoglycan 1)
    TACAATAAAC11131.20.0009071PGRMC2Progesterone receptor membrane component 2
    AGTTTCCCAA1012.11.20.000279929HSGP25L2Ggp25L2 protein
    TCTTCTGCCA69.41.70.00286392KIAA1402CSGlcA-T KIAA1402 protein
    TTCCTCCTTT>77.200.000151155TM6SF1Transmembrane 6 superfamily member 1
    TTACTTATAC>66.300.000159TNFRSF1ATumor necrosis factor receptor superfamily, member 1A
    TAAGAAAATG>65.800.001443435CDH11Cadherin 11, type 2, OB-cadherin (osteoblast)
    AGAACCTTAA>54.900.003181244HLA-AMajor histocompatibility complex, class I, A
    GCCCTTTCTC325.27.50.0007835MRC2Mannose receptor, C type 2
    GTTGTGGTTA260.328.50.00075415B2Mβ-2-microglobulin
Transcription
    TACAGAGGGA89.41.20.000406096ZNF216Zinc finger protein 216
    AAAAGATACT67.61.20.00382071CITED2Cbp/p300-interacting transactivator, with Glu/Asp-rich COOH-terminal domain, 2
    GCCATATTAT>55.400.002170752CRIM1Cysteine-rich motor neuron 1
    CTCGAATAAA>44.500.00434871ZFHX1BZinc finger homeobox 1b
Others
    AATTTTCATT105.80.60.006339024LOC253827Hypothetical protein LOC253827
    TTTTGTATTT105.80.60.006439190C14orf31Chromosome 14 open reading frame 31
    GGTGAAGACA78.51.20.00126951RUSC2RUN and SH3 domain containing 2
    CCCTGATTTT619.83.50.000183684EIF4G2Eukaryotic translation initiation factor 4 γ, 2
    ATGTGAAGAA66.71.20.00813662MGC5508Hypothetical protein MGC5508
    GAATAAATGT67.21.20.005497972FKBP9FK506 binding protein 9, 63 kDa
    GCTGTTTTGT>66.300.000426312AMOTL2Angiomotin like 2
    TTCCGGTTCC591.70.003172609NUCB1Nucleobindin 1
    GTGGCTGAAA>54.900.003401929rpL10ribosomal protein L10
    CTTAATCCTG430.68.10.000298275SLC38A2Solute carrier family 38, member 2
    GAAATAATGG418.44.60.000343879SPANXCSPANX family, member C
    AAGGCAATTT412.62.90.001301626FLJ11739Homo sapiens cDNA FLJ11739 fis
    AAGTGAAACA410.32.90.00693659ERP70Protein disulfide isomerase related protein (calcium-binding protein, intestinal-related)
    TTAAAACAAA>4400.01370610WACWW domain containing adaptor with coiled coil
    AAAACATTCT267.532.50.00323562DKFZp564K142DKFZp564K142 implantation-associated protein
  • * Fold down-regulation of SHEP-2/SHEP-21N.

  • The expression in SHEP-2 and SHEP-21N is given in number of tags normalized per 20,000 tags.

  • Ps were calculated with the Monte Carlo simulation of the SAGE software ( 40).