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SAGE Genie
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Cancer Genome Characterization Initiative

Visit the database of genomic characterization data for multiple tumor types.


SAGE Experimental Viewer (SEV)

The SAGE Experimental Viewer (SEV) automatically sets up the Digital Gene Expression Displayer (DGED) comparison between matched pairs of libraries, derived from a specific experiment and its control. On the DGED set up page, the user can select the statistical parameters of significance and link to each Library Info page. The experiments fall into the following categories:

Anatomic Comparisons
Microenvironment
Oncogenes and Tumor Suppressors
Tumor vs Metastasis
Tumor vs Normal

Experiment Name Description/Reference DGED Results

  Anatomic Comparisons  
Cortex_Cerebellum Transcripts differentially expressed between bulk cortex and bulk cerebellum, from the same rapid autopsy brain. (1) Short SAGE Cortex_Cerebellum DGED
Cortex_Thalamus Transcripts differentially expressed between bulk cortex and bulk thalamus, from the same rapid autopsy brain. (1) Short SAGE Cortex_Thalamus DGED
  Microenvironment  
Estrogen_10 Transcriptional influence of 10 hours of estradiol on cultured breast cancer cells (MCF7). (No reference) Short SAGE Estrogen_10 DGED
Estrogen_16 Transcriptional influence of 16 hours of estrogen on estrogen responsive cultured breast cancer cells (ZR75-1) compared to untreated cells. (2) Short SAGE Estrogen_16 DGED
Hypoxia Comparison between a glioblastoma line, cultured under hypoxic conditions (1.5% oxygen) and known to be hypoxia responsive for the secretion of VEGF, and the same cell line grown in a conventional incubator in normal atmospheric oxygen. (3). Short SAGE Hypoxia DGED
Senescence Comparison of normal prostate cells grown in culture that are arrested either by senescence or due to confluence. (4). Short SAGE Senescence DGED
Tamoxifen_16 Transcriptional influence of 16 hours of tamoxifen on estrogen responsive cultured breast cancer cells (ZR75-1) compared to untreated cells. (2) Short SAGE Tamoxifen_16 DGED
  Oncogenes and Tumor Suppresors  
Beta-catenin Comparison between cultured 293 kidney embryonic cells overexpressing normal beta-catenin using an inducible system and the same cell line without induction, therefore not expressing beta-catenin. (No reference) Short SAGE Beta-catenin DGED
EGFR Comparison between a glioblastoma cell line expressing a mutant form of EGFR and the same cell line expressing LacZ as control. (5) Short SAGE EGFR DGED
  Tumor vs Metastasis  
Breast_TM1 Comparison of a primary breast carcinoma and the metastatic tumor to the lymph node, from the same patient. (6, 7) Short SAGE Breast_TM1 DGED
Breast_TM2 Comparison of a primary breast carcinoma and the metastatic tumor to the lymph node, from the same patient. (6, 7) Short SAGE Breast_TM2 DGED
  Tumor vs Normal  
Breast_CN1 Comparison between affinity purified breast ductal carcinoma (DCIS) in situ tumor cells and purified normal epithelium obtained from the same patient after surgery. (6, 7) Short SAGE Breast_CN1 DGED
Colon_CN1 Comparison of matched normal and tumor tissue from a patient with colon adenocarcinoma. The tumor is a bulk sample, and the normal tissue is taken from the colonic epithelium removed from the adjacent normal colon during the surgery for tumor resection. (8) Short SAGE Colon_CN1 DGED
Colon_CN2 Comparison of matched normal and tumor tissue from a patient with colon adenocarcinoma. The tumor is a bulk sample, and the normal tissue is taken from the colonic epithelium removed from the adjacent normal colon during the surgery for tumor resection. (8) Short SAGE Colon_CN2 DGED
Prostate_CN1 Comparison of matched normal and tumor tissue from a single manually microscope dissected prostate tumor and adjacent normal prostate epithelium. (No reference) Short SAGE Prostate_CN1 DGED

References

  1. Siu IM, Lal A, and Riggins GJ. Database for Normal Gene Expression in the Human Brain. Gene Expression Patterns 1:33-38, 2001.
  2. Seth P, Krop I, Porter D, Polyak K. Novel estrogen and tamoxifen induced genes identified by SAGE. Oncogene 21, 836-43 (2002).
  3. A. Lal A, Peters H, St Croix B, Haroon ZA, Dewhirst MW, Strausberg RL, Kaanders JH, van der Kogel AJ, Riggins GJ. Transcriptional Response to Hypoxia in Human Tumors. J Natl Cancer Inst. 2001 Sep 5;93(17):1337-43.
  4. Untergasser G, Koch HB, Menssen A, Hermeking H. Characterization of epithelial senescence by serial analysis of gene expression: identification of genes potentially involved in prostate cancer. Cancer Res 62, 6255-62 (2002)
  5. Lal A, Glazer CA, Martinson HM, Friedman HS, Archer GE, Sampson JH, Riggins GJ. Mutant epidermal growth factor receptor up-regulates molecular effectors of tumor invasion. Cancer Res. 62,3335-9 (2002)
  6. Porter DA, Krop IE, Nasser S, Sgroi D, Kaelin CM, Marks JR, Riggins G, Polyak K. A SAGE view of breast tumor progression. Cancer Res. 61, 5697-702 (2001).
  7. Krop IE, Sgroi D, Porter DA, Lunetta KL, LeVangie R, Seth P, Kaelin CM, Rhei E, Bosenberg M, Schnitt S, Marks JR, Pagon Z, Belina D, Razumovic J, Polyak K. HIN-1, a putative cytokine highly expressed in normal but not cancerous mammary epithelial cells. PNAS 98, 9796-801 (2001). Epub 2001 Jul 31.
  8. Zhang L, Zhou W, Velculescu VE, Kern SE, Hruban RH, Hamilton SR, Vogelstein B, Kinzler KW. Gene expression profiles in normal and cancer cells. Science 276, 1268-1272 (1997)