Article Figures & Data
Figures
- Fig. 1.
Experimental scheme and summary of results. Some of the known genes were represented by more than one EST clone.
- Fig. 2.
Comparisons between WT and Null cells or between Null+MYC and Null cells during log-phase growth. A, comparison of WT and Null cells at log phase. A section of the microarray is shown. Total RNA from WT cells was labeled with cy5-dUTP; total RNA from Null cells was labeled with cy3-dUTP. B, comparison of Null+MYC and Null cells at log phase. The same section of the microarray as in A is shown. Total RNA from Null+MYC cells was labeled with cy5-dUTP; total RNA from Null cells was labeled with cy3-dUTP. C, scatter plot of the calibrated ratios (log scale) in the two independent comparisons between WT cells and Null cells. D, scatter plot of the calibrated ratios (log scale) in the comparisons between WT cells and Null cells (vertical axis) and between Null+MYC cells and Null cells (horizontal axis).
- Fig. 3.
Confirmation of differentially expressed genes in microarray analysis by Northern hybridizations. (−/−), Null cells; (+/+), WT cells; (−/−)+Myc, Null+MYC cells; (+/+)+Myc, WT+MYC cells. The cDNA probes were: i, c-myc; ii, CPD (carboxypeptidase D); iii, Cyclin D1; iv, GCN1; v, PGAM (peptidylglycine α-amidating monooxygenase); vi, rp-S12 (ribosomal protein S12); vii, rp-L6 (ribosomal protein L6); viii, NPM (nucleophosmin or nucleolar phosphoprotein B23); ix, α-NAC (nascent polypeptide associated complex); x, LDH-A; xi, 28S rRNA (inverted picture of agarose gel stained with ethidium bromide solution); xii, actin.
Tables
- Table 1
Genes up-regulated by c-Myca
No. Gene name Function Ratiob -Serac c-myc Transcription 2.6 1 Cdc2 d Cell cycle 3.6 2 cdk regulatory subunit 2 (CKS-2) Cell cycle 3.4 3 Proliferating cell nuclear antigen (PCNA) Cell cycle 3.2 4 AIM-1 Cell cycle 2.7 5 Mitotic feedback protein control protein Cell cycle 4.2 6 Adenine nucleotide translocator Apoptosis 3.4 7 Proliferating cell-associated mRNA Cell growth 2.5 8 JTV-1 protein Cell growth 2.6 9 Lens epithelial protein Cell growth 3.4 10 rab GDP-dissociation inhibitor β Signaling 2.6 11 rhoB Signaling 4.0 12 Protein phosphatase-1 γ1 (pp-1γ1) Signaling 2.5 13 Macrophage migration inhibitory factor (MIF) Signaling 2.9 14 Hyaluronan synthase 2 Signaling 2.6 15 Nucleosome assembly protein Chromosomal 3.0 2.7 16 Histone H2a.z Chromosomal 3.4 17 HMG-17 non-histone chromosomal protein Chromosomal 2.8 18 APEX endonuclease DNA repair 4.7 19 DNA polymerase α DNA replication 3.8 2.9 20 Rb-binding protein (RBP1) Transcription 3.7 3.1 21 Transcriptional regulatory factor (α-NAC) Transcription 3.0 22 Transducin-like enhancer protein 4 (Grg-4) Transcription 2.5 23 C-1 putative transcription factor Transcription 2.6 24 Rat Y-Box binding protein α (RYB-α) Transcription 2.7 25 Glutamine-rich factor 1 Transcription 2.7 26 Small nuclear ribonucleoprotein Sm D3 RNA processing 2.9 27 Heterogeneous nuclear ribonucleoprotein G RNA processing 2.4 28 Splicing factor SC35 RNA processing 2.9 29 Leucyl-tRNA synthetase homologue Protein synthesis 2.9 30 Ribosomal phosphoprotein P1 Protein synthesis 3.2 31 Ribosomal protein L5 Protein synthesis 4.7 2.7 32 Ribosomal protein L6 Protein synthesis 3.6 33 Ribosomal protein L7 Protein synthesis 4.4 2.3 34 Ribosomal protein L7a Protein synthesis 4.2 2.4 35 Ribosomal protein L9 Protein synthesis 3.4 36 Ribosomal protein L10 Protein synthesis 4.0 2.2 37 Ribosomal protein L12 Protein synthesis 3.1 38 Ribosomal protein L19 Protein synthesis 2.8 39 Ribosomal protein L21 Protein synthesis 3.4 2.2 40 Ribosomal protein L22 Protein synthesis 3.3 41 Ribosomal protein L23 Protein synthesis 4.6 2.2 42 Ribosomal protein L26 Protein synthesis 4.0 43 Ribosomal protein L27 Protein synthesis 3.0 44 Ribosomal protein L30 Protein synthesis 3.7 45 Ribosomal protein L32 Protein synthesis 4.3 46 Ribosomal protein L35 Protein synthesis 4.0 47 Ribosomal protein L41 Protein synthesis 3.5 2.5 48 Ribosomal protein L44 Protein synthesis 5.4 2.4 49 Ribosomal protein S4 Protein synthesis 3.6 50 Ribosomal protein S7 Protein synthesis 3.7 51 Ribosomal protein S9 Protein synthesis 3.3 52 Ribosomal protein S12 Protein synthesis 4.2 53 Ribosomal protein S13 Protein synthesis 4.8 54 Ribosomal protein S15a Protein synthesis 3.1 55 Ribosomal protein S16 Protein synthesis 2.8 56 Ribosomal protein S18 Protein synthesis 4.1 3 57 Ribosomal protein S19 Protein synthesis 3.0 58 Ribosomal protein S20 Protein synthesis 4.1 2.2 59 Ribosomal protein S23 Protein synthesis 3.5 60 Elongation factor 2 (EF-2) Protein synthesis 2.8 2.3 61 Signal recognition particle subunit (SRP) Protein synthesis 4.9 2.2 62 Breast basic conserved protein 1 Protein synthesis 4.5 63 RNA helicase p68 Protein synthesis 3.9 64 Nucleophosmin (NPM; B23) Protein synthesis 4.2 2.5 65 Spermidine synthase Protein/RNA synthesis 3.7 66 Cyclophilin-40 (40 kD) Protein folding 2.8 67 Cyclophilin (18 kD) Protein folding 2.7 68 Ran/TC4 GTP-binding nuclear protein Protein/RNA transport 2.9 69 Ran/TC4 binding protein (RanBP1) Protein/RNA transport 3.2 70 Secretory carrier-associated protein 2 Protein transport 3.2 71 Heat shock protein 60 (HSP60) d Protein folding 5.0 72 Heat shock protein 90 (HSP90) Protein folding 3.3 73 Chaperonin-containing TCP-1 zeta subunit Protein folding 2.9 74 E2-EPF ubiquitin-carrier protein Protein degradation 2.6 75 Ubiquitin-like protein SMT3B Protein degradation 2.3 76 Ubiquitin Protein degradation 4.2 77 R-IOTA (proteasome subunit) Protein degradation 2.9 78 Phosphorylation regulatory protein HP-10 Protein phosphorylation 2.6 79 Lactate dehydrogenase (LDH-A) d Metabolism 3.1 80 Enolase-α Metabolism 2.6 81 Glycerate dehydrogenase (GDH) Metabolism 2.6 82 Thioredoxin Metabolism 2.3 - Table 1A
Continued
No. Gene name Function Ratiob -Serac 83 Thioredoxin-dependent peroxide reductase Metabolism 2.3 84 Cytochrome c Metabolism 2.7 85 Heme oxygenase-2 Metabolism 3.0 86 β-1,4-Galactosyltransferase Metabolism 3.3 87 Sarcosine dehydrogenase Metabolism 2.9 88 Inosine 5′-monophosphate dehydrogenase Metabolism 3.9 2.5 89 PEP carboxykinase Metabolism 5.9 90 Acyl-CoA-binding protein Metabolism 2.5 91 ATPase inhibitor protein IF1 Metabolism 3.0 92 Microsomal glutathione-S-transferase 3 Metabolism 3.8 2.3 93 Cysteine-rich intestinal protein (CRIP) Zinc absorption 3.3 94 Microtubule-associated protein 4 (MAP4) Cell structure 2.7 95 Peripherin Cell structure 2.9 96 Voltage-dependent anion channel-like protein Channel 2.3 -
a A complete list of the differentially expressed genes, including unknown ESTs, can be found on our web site (http://www-dcs.nci.nih.gov/research/labdata/Liulab.html).
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b The average of ratios in both WT/Null and Null+MYC/Null comparisons during log-phase growth.
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c The ratios in the comparison between WT cells and Null cells under the serum starvation condition.
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d Gene reported previously to be a Myc target.
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- Table 2
Genes down-regulated by c-Myca
No. Gene name Function Ratiob -Serac 1 Cyclin D1d Cell cycle 0.28 2 PINCH protein Apoptosis 0.35 0.29 3 Protein phosphatase 2A regulatory subunit ε Signaling 0.22 4 Protein kinase C-binding protein (Enigma) Signaling 0.36 5 Mitogen activated protein kinase-1 (ERK1) Signaling 0.30 6 Protein kinase (MEKK) Signaling 0.40 7 RAC-α serine/threonine kinase (RAC-PK-α) Signaling 0.10 8 RAC-β serine/threonine kinase (RAC-PK-β) Signaling 0.20 9 Thy-1 glycoprotein Signaling 0.38 10 T-cell receptor, T3-epsilon glycoprotein Signaling 0.33 0.20 11 unr protein (upstream of N-ras) DNA binding 0.10 12 Calcium-binding protein (nucleobindin, NUCB1) DNA binding 0.24 13 Vascular actin single-stranded DNA-binding factor Transcription 0.24 14 Retinoic acid receptor α2 Transcription 0.40 15 Sp3 transcription factor Transcription 0.19 16 Ubiquitous Kruppel-like factor Transcription 0.26 17 Zinc finger X-linked protein ZXDB Transcription 0.34 18 Red-1 nuclear protein Transcription 0.16 19 Female sterile homeotic homolog RING3 Transcription 0.32 20 Heterogeneous nuclear ribonucleoprotein H RNA processing 0.19 21 Nuclear ribonucleoparticle-associated protein RNA processing 0.23 22 Paraneoplastic encephalomyelitis antigen hud RNA processing 0.20 0.09 23 GCN1 (translational activator) Protein synthesis 0.36 24 α-B-crystallin Protein folding 0.23 25 Ischemia-responsive 94 kDa protein Protein folding 0.11 26 Carboxypeptidase D (CPD) Protein processing 0.23 27 ATP-dependent metalloprotease FtsH1 Protein degradation 0.09 28 Peptidylglycine α-amidating monooxygenase Protein modification 0.34 29 ARL-6 interacting protein-1 (Aip-1) Protein trafficking 0.24 30 Lysosomal membrane glycoprotein (LAMP-1) Metabolism 0.07 31 ATP-specific succinyl-CoA synthetase-β Metabolism 0.12 32 B-locus C-type lectin Metabolism 0.43 33 β-1,3-Galactosyltransferase Metabolism 0.37 34 Long chain fatty acid-CoA ligase Metabolism 0.26 35 Ganglioside GM2 activator protein Lipid degradation 0.23 0.36 36 MHC class II RT1.B α chain Immune response 0.36 0.36 37 MHC class II RT1.D β chain Immune response 0.23 0.17 38 MHC Class I α-chain antigend Immune response 0.31 39 NCAM-140/180 neural cell adhesion molecule Adhesion 0.28 0.36 40 Peroxisomal farnesylated protein (PxF) Cell structure 0.36 41 Moesin Cytoskeletal 0.40 42 Tropomyosin α chaind Cytoskeletal 0.25 43 Na-K-Cl cotransporter Channel 0.16 44 Impact Paternally expressed 0.28 45 Tumor protein D52 Expressed in tumor 0.40 46 Proline-rich protein Unknown 0.38 -
a A complete list of the differentially expressed genes, including unknown ESTs, can be found on our web site (http://www-dcs.nci.nih.gov/research/labdata/Liulab.html).
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b The average of ratios in both WT/Null and Null+MYC/Null comparisons during log-phase growth.
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c The ratios in the comparison between WT cells and Null cells under the serum starvation condition.
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d Gene reported previously to be a Myc target.
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- Table 3
Genes regulated by overexpressed c-Myca
No. Gene name Function Ratiob c-myc Transcription 4.5 1 PCAF associated factor-β Transcription 2.3 2 DNA polymerase αc DNA synthesis 3.6 3 Cyclin-dependent kinase-4 (cdk-4)d Cell cycle 2.9 4 Centromere protein (27 kD) Cell cycle 2.5 5 Phosphatidylinositol 4-phosphate 5-kinase Iα Signaling 3.5 6 Sigma receptor type 1 (SigmaR1) Signaling 2.6 7 Heparin-binding growth factor 8 (HBGF-8) Signaling 2.4 8 Scavenger receptor class B type I (SR-B1) Metabolism 2.5 9 Stearyl-CoA desaturase 2 Metabolism 5.6 10 Thioredoxin-dependent peroxide reductasec Metabolism 2.4 11 Fibrillin 2 Extracellular matrix 2.4 12 PINCH proteinc Apoptosis 0.32 13 GADD45d DNA repair 0.45 14 Histone H3.3B Chromosomal 0.37 15 HSP27 Protein folding 0.46 16 Serine protease Protein degradation 0.41 17 Ubiquitin-homology domain protein (PIC1) Protein degradation 0.35 18 Peripheral-type benzodiazepine receptor Metabolism 0.44 19 Drosophila frizzled gene homologue Signaling 0.47 20 Nuclear dual-specificity phosphatase Signaling 0.30 21 Prolactin receptor associated protein Signaling 0.42 22 γ-PAK Signaling 0.21 23 PAK-interacting exchange factor (β-PIX) Signaling 0.23 24 PE31/TALLA Signaling 0.35 25 Thy-I glycoproteinc Signaling 0.41 26 Vascular endothelial growth factor D Signaling 0.44 27 Channel integral membrane protein 28 Water channel 0.37 28 Osteonectin Cell growth 0.33 29 UP50 (EGF-like serum-suppressed gene) Cell growth 0.34 30 TGF-β responsive adhesion-inhibition gene Tumor suppression 0.29 31 Thrombospondind Metastasis 0.23 32 Collagen α1(V) Cell structure 0.32 -
a A complete list of the differentially expressed genes, including unknown ESTs, can be found on our web site (http://www-dcs.nci.nih.gov/research/labdata/Liulab.html).
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b The average of ratios in comparison between WT+MYC and WT cells during log-phase growth. Values of more than 1 represent c-Myc up-regulated genes. Values of less than 1 represent the c-Myc down-regulated genes.
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c Genes present in Tables 1 <$REFLINK> and 2 <$REFLINK> .
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d Gene reported previously to be a Myc target.
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Volume 60, Issue 21
