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SAGE Genie
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SAGE References

  1. Velculescu VE, Zhang L, Vogelstein B, and Kinzler KW. (1995) Serial analysis of gene expression. Science, 270, 484-487. Original paper describing SAGE.

  2. Velculescu VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett D Jr, Hieter P, Vogelstein B, Kinzler, KW. (1997) Characterization of the yeast transcriptome. Cell 88: 243-251. Use of SAGE to describe the first analysis of a eukaryotyic transcriptome.

  3. Zhang L, Zhou W, Velculescu VE, Kern S, Hruban R, Hamilton S, Vogelstein B, Kinzler, KW. (1997) Gene expression profiles in normal and cancer cells. Science 276: 1268-1272. Use of SAGE to perform the first global analysis of gene expression in human cancer.

  4. Lal A, Sui I-M, and Riggins G. (1999) Serial Analysis of Gene Expression: Probing transcriptomes for molecular targets. Current Opinion in Molecular Therapeutics, 1, 720-726. General SAGE review.

  5. Lal A, Lash AE, Altschul SF, Velculescu V, Zhang L, McLendon RE, Marra MA, Prange C, Morin PJ, Polyak K, Papadopoulos N, Vogelstein B, Kinzler KW, Strausberg RL, Riggins GJ. (1999) A public database for gene expression in human cancers. Cancer Res. 59, 5403-7. Original description of the CGAP SAGE Project, and use of SAGE for a public database.

  6. Velculescu VE, Madden SL, Zhang L, Lash AE, Yu J, Rago C, Lal A, Wang CJ, Beaudry GA, Ciriello KM, Cook BP, Dufault MR, Ferguson AT, Gao Y, He TC, Hermeking H, Hiraldo SK, Hwang PM, Lopez MA, Luderer HF, Mathews B, Petroziello JM, Polyak K, Zawel L, Kinzler KW, et al. (1999) Analysis of human transcriptomes. Nature Genetics 23, 387-388.

  7. Madden SL, Wang CJ, and Landes G. (2000) Serial analysis of gene expression: from gene discovery to target identification. Drug Discov Today, 5, 415-425. General SAGE review.

  8. Velculescu VE, Vogelstein B, and Kinzler KW. (2000) Analysing uncharted transcriptomes with SAGE. Trends Genet, 16, 423-425. General SAGE review.

  9. Powell J. (2000) SAGE. The serial analysis of gene expression. Methods Mol Biol, 99, 297-319. General SAGE review.

  10. Riggins GJ. (2001) Using Serial Analysis of Gene Expression to identify tumor markers and antigens. Dis Markers 17, 41-8. Review of SAGE for tumor marker discovery.

  11. Boon K, Osório E, Greenhut SF, Schaefer CF, Shoemaker J, Polyak K, Morin PJ, Buetow KH, Strausberg RL, de Souza SJ, and Riggins GJ. (2002) An anatomy of normal and malignant gene expression. Proc Natl Acad Sci 99, 11287-92. Original reference for the bioinformatics and tools for SAGE Genie.

  12. Liang P. (2002) SAGE Genie: a suite with panoramic view of gene expression. Proc Natl Acad Sci 99, 11547-8. Epub 2002 Aug 23. Commentary on the previous PNAS paper.

  13. Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, Kinzler KW, Velculescu VE. (2002) Using the transcriptome to annotate the genome. Nature Biotechnology 20: 508-12. Original description of the LongSAGE approach.

  14. Buckhaults P, Zhang Z, Chen YC, Wang TL, St Croix B, Saha S, Bardelli A, Morin PJ, Polyak K, Hruban RH, Velculescu VE, Shih IeM. (2003) Identifying tumor origin using a gene expression-based classification map. Cancer Res. 63, 4144-9.

  15. Porter D, Lahti-Domenici J, Keshaviah A, Bae YK, Argani P, Marks J, Richardson A, Cooper A, Strausberg R, Riggins GJ, Schnitt S, Gabrielson E, Gelman R, Polyak K. (2003) Molecular markers in ductal carcinoma in situ of the breast. Mol Cancer Res. 1, 362-75.

  16. Porter D, Weremowicz S, Chin K, Seth P, Keshaviah A, Lahti-Domenici J, Bae YK, Monitto CL, Merlos-Suarez A, Chan J, Hulette CM, Richardson A, Morton CC, Marks J, Duyao M, Hruban R, Gabrielson E, Gelman R, Polyak K.(2003) A neural survival factor is a candidate oncogene in breast cancer. Proc Natl Acad Sci 100, 10931-6. Epub 2003 Sep 02.

  17. Boon K, Edwards JB, Siu IM, Olschner D, Eberhart CG, Marra MA, Strausberg RL, Riggins GJ.(2003) Comparison of medulloblastoma and normal neural transcriptomes identifies a restricted set of activated genes. Oncogene 22, 7687-94.

  18. Cerutti JM, Delcelo R, Amadei MJ, Nakabashi C, Maciel RM, Peterson B, Shoemaker J, Riggins GJ. (2004) A preoperative diagnostic test that distinguishes benign from malignant thyroid carcinoma based on gene expression. Clin Invest. 113, 1234-42.

  19. Georgantas RW 3rd, Tanadve V, Malehorn M, Heimfeld S, Chen C, Carr L, Martinez-Murillo F, Riggins G, Kowalski J, Civin CI. (2004) Microarray and serial analysis of gene expression analyses identify known and novel transcripts overexpressed in hematopoietic stem cells. Cancer Res. 64, 4434-41.

  20. Boon K, Eberhart CG, Riggins GJ. (2005) Genomic amplification of orthodenticle homologue 2 in medulloblastomas. Cancer Res. 65, 703-7.

  21. 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.

  22. Siu IM, Lal A, Riggins GJ. A database for regional gene expression in the human brain. Brain Res Gene Expr Patterns. 2001 Aug;1(1):33-8.

  23. Lu J, Lal A, Merriman B, Nelson S, Riggins G. A comparison of gene expression profiles produced by SAGE, long SAGE, and oligonucleotide chips. Genomics. 2004 Oct;84(4):631-6.

  24. Strausberg RL, Simpson AJ, Old LJ, Riggins GJ. Oncogenomics and the development of new cancer therapies. Nature. 2004 May 27;429(6990):469-74. Review.

  25. Cerutti JM, Latini FR, Nakabashi C, Delcelo R, Andrade VP, Amadei MJ, Maciel RM, Hojaij FC, Hollis D, Shoemaker J, Riggins GJ. Diagnosis of suspicious thyroid nodules using four protein biomarkers. Clin Cancer Res. 2006 Jun 1;12(11 Pt 1):3311-8.

  26. 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. 2002 Jun 15;62(12):3335-9.

  27. Loging WT, Lal A, Siu IM, Loney TL, Wikstrand CJ, Marra MA, Prange C, Bigner DD, Strausberg RL, Riggins GJ. Identifying potential tumor markers and antigens by database mining and rapid expression screening. Genome Res. 2000 Sep;10(9):1393-402.

  28. Kuan CT, Wakiya K, Dowell JM, Herndon JE 2nd, Reardon DA, Graner MW, Riggins GJ, Wikstrand CJ, Bigner DD. Glycoprotein nonmetastatic melanoma protein B, a potential molecular therapeutic target in patients with glioblastoma multiforme. Clin Cancer Res. 2006 Apr 1;12(7 Pt 1):1970-82.

  29. Riggins GJ, Strausberg RL. Genome and genetic resources from the Cancer Genome Anatomy Project. Hum Mol Genet. 2001 Apr;10(7):663-7. Review.

  30. Cuevas IC, Slocum AL, Jun P, Costello JF, Bollen AW, Riggins GJ, McDermott MW, Lal A. Meningioma transcript profiles reveal deregulated Notch signaling pathway. Cancer Res. 2005 Jun 15;65(12):5070-5.

  31. Weeraratna AT, Becker D, Carr KM, Duray PH, Rosenblatt KP, Yang S, Chen Y, Bittner M, Strausberg RL, Riggins GJ, Wagner U, Kallioniemi OP, Trent JM, Morin PJ, Meltzer PS. Generation and analysis of melanoma SAGE libraries: SAGE advice on the melanoma transcriptome. Oncogene. 2004 Mar 18;23(12):2264-74.

  32. Boon K, Edwards JB, Eberhart CG, Riggins GJ. Identification of astrocytoma associated genes including cell surface markers. BMC Cancer. 2004 Jul 21;4:39.

  33. Perez-Plasencia C, Riggins G, Vazquez-Ortiz G, Moreno J, Arreola H, Hidalgo A, Pina-Sanchez P, Salcedo M. Characterization of the global profile of genes expressed in cervical epithelium by Serial Analysis of Gene Expression (SAGE). BMC Genomics. 2005 Sep 19;6:130.

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