Description of SAGE method
	SAGE Reviews
	Cancer studies
	Human disease
	Pathway analysis
	Plant and model organisms
	Bioinformatics and transcriptome analysis
	Technological advances

Description of SAGE method

Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, Kinzler KW, Velculescu, VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE, Hieter P, Vogelstein B, and Kinzler KW (1997). Characterization of the yeast transcriptome. Cell 88, 243-251

Velculescu VE, Zhang L, Vogelstein B, and Kinzler KW (1995). Serial Analysis Of Gene Expression. Science 270, 484-487

Reviews

Patino WD, Mian OY, Hwang PM. Serial analysis of gene expression: technical considerations and applications to cardiovascular biology. Circ Res. 2002 Oct 4;91(7):565-9.

Li J, Chen YG, Kong XY. [New progress of serial analysis of gene expression] Sheng Wu Gong Cheng Xue Bao. 2001 Nov;17(6):613-6. Review. Chinese.

Polyak K and Riggins G. Gene discovery using the Serial Analysis of gene expression Technique: Implications for cancer research. J or Clinical Oncologyl 2001 June:

Riggins GJ, Strausberg RL Genome and genetic resources from the Cancer Genome Anatomy Project. Hum Mol Genet. 2001 Apr 1;10(7):663-7.

Bartlett J. Technology evaluation: SAGE, Genzyme molecular oncology. Curr Opin Mol Ther. 2001 Feb;3(1):85-96. Review.

Velculescu VE, Vogelstein B, Kinzler KW. Analysing uncharted transcriptomes with SAGE. Trends Genet. 2000 Oct;16(10):423-5

The Netherlands. Baas F, Tabak HF A tale of tags: report on a HUGO/EU SAGE workshop, 29 January-1 February 1999, Hilversum, Eur J Hum Genet 1999 May-Jun;7(4):510-2

Velculescu VE. Tantalizing Transcriptomes – SAGE and its use in global gene expression analysis. Science 1999 Nov 19; 286: 1491-1492

Bertelsen AH, Velculescu VE (1998). High-throughput gene expression analysis using SAGE. Drug Discovery Today 3: 152-159

Adams MD (1996). Serial analysis of gene expression: ESTs get smaller. Bioessays 4:261-2

Cancer studies

Bosma AJ, Weigelt B, Lambrechts AC, Verhagen OJ, Pruntel R, Hart AA, Rodenhuis S, van 't Veer LJ. Detection of circulating breast tumor cells by differential expression of marker genes. Clin Cancer Res. 2002 Jun;8(6):1871-7.

El-Rifai W, Moskaluk CA, Abdrabbo MK, Harper J, Yoshida C, Riggins GJ, Frierson HF Jr, Powell SM. Gastric cancers overexpress S100A calcium-binding proteins. Cancer Res. 2002 Dec 1;62(23):6823-6.

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. 2002 Nov 1;62(21):6255-62.

Gu Z, Lee RY, Skaar TC, Bouker KB, Welch JN, Lu J, Liu A, Zhu Y, Davis N, Leonessa F, Brunner N, Wang Y, Clarke R. Association of interferon regulatory factor-1, nucleophosmin, nuclear factor-kappaB, and cyclic AMP response element binding with acquired resistance to Faslodex (ICI 182,780). Cancer Res. 2002 Jun 15;62(12):3428-37.

Bosma AJ, Weigelt B, Lambrechts AC, Verhagen OJ, Pruntel R, Hart AA, Rodenhuis S, Van 't Veer LJ. Detection of Circulating Breast Tumor Cells by Differential Expression of Marker Genes. Clin Cancer Res. 2002 Jun;8(6):1871-1877.

Mitas M, Mikhitarian K, Hoover L, Lockett MA, Kelley L, Hill A, Gillanders WE, Cole DJ. Prostate-Specific Ets (PSE) factor: a novel marker for detection of metastatic breast cancer in axillary lymph nodes. Br J Cancer. 2002 Mar 18;86(6):899-904.

Iacobuzio-Donahue CA, Maitra A, Shen-Ong GL, van Heek T, Ashfaq R, Meyer R, Walter K, Berg K, Hollingsworth MA, Cameron JL, Yeo CJ, Kern SE, Goggins M, Hruban RH.

Discovery of novel tumor markers of pancreatic cancer using global gene expression technology. Am J Pathol. 2002 Apr;160(4):1239-49. Hunter S, Young A, Olson J, Brat DJ, Bowers G, Wilcox JN, Jaye D, Mendrinos S, Neish A. Differential expression between pilocytic and anaplastic astrocytomas: identification of apolipoprotein D as a marker for low-grade, non-infiltrating primary CNS neoplasms. J Neuropathol Exp Neurol. 2002 Mar;61(3):275-81.

Caldwell MC, Hough C, Furer S, Linehan WM, Morin PJ, Gorospe M. Serial analysis of gene expression in renal carcinoma cells reveals VHL-dependent sensitivity to TNFalpha cytotoxicity. Oncogene. 2002 Jan 31;21(6):929-36.

Argani P, Iacobuzio-Donahue C, Ryu B, Rosty C, Goggins M, Wilentz RE, Murugesan SR,Leach SD, Jaffee E, Yeo CJ, Cameron JL, Kern SE, Hruban RH. Mesothelin is overexpressed in the vast majority of ductal adenocarcinomas of the pancreas: identification of a new pancreatic cancer marker by serial analysis of gene expression (SAGE). Clin Cancer Res. 2001 Dec;7(12):3862-8.

Nacht M, Dracheva T, Gao Y, Fujii T, Chen Y, Player A, Akmaev V, Cook B, Dufault M, Zhang M, characteristics of non-small cell lung cancer. Proc Natl Acad Sci U S A. 2001 Dec 18;98(26):15203-8.

Zheng F, Cai W, Mitsuhashi T, Vlassara H. Lysozyme enhances renal excretion of advanced a potential AGE sequestration therapy for diabetic nephropathy? Mol Med. 2001 Nov;7(11):737-47.

Touloukian CE, Leitner WW, Robbins PF, Rosenberg SA, Restifo NP. Identification of androgen-regulated genes in the prostate cancer cell line LNCaP by serial analysis of gene expression and proteomic analysis. Proteomics. 2001 Oct;1(10):1327-38.

Waghray A, Feroze F, Schober MS, Yao F, Wood C, Puravs E, Krause M, Hanash S, Chen YQ. Identification of androgen-regulated genes in the prostate cancer cell line LNCaP by serial analysis of gene expression and proteomic analysis. Proteomics. 2001 Oct;1(10):1327-38.

Porter DA, Krop IE, Nasser S, Sgroi D, Kaelin CM, Marks JR, Riggins G, Polyak K. A SAGE (serial analysis of gene expression) view of breast tumor progression. Cancer Res.2001 Aug 1;61(15):5697-702.

Vandeputte DA, Meije CB, van Dartel M, Leenstra S, IJlst-Keizers H, Das PK, Troost D, Bosch DA, Baas F, Hulsebos TJ.GOA, a novel gene encoding a ring finger B-box coiled-coil protein, is overexpressed in astrocytoma.Biochem Biophys Res Commun.2001 Aug 24;286(3):574-9.

Krop IE, Sgroi D, Porter DA, Lunetta KL, LeVangie R, Seth P, Kaelin CM, Rhei E, Bosenberg M, Schnitt S,Bittencourt Rosas SL, Caballero OL, Dong SM, da Costa Carvalho Mda G, Sidransky D,Jen J. Methylation status in the promoter region of the human PGP9.5 gene in cancer and normal tissues. Cancer Lett. 2001 Sep 10;170(1):73-9. Vandeputte DA, Meije CB, van Dartel M, Leenstra S, IJlst-Keizers H, Das PK, Troost D, Bosch DA, Baas F, Hulsebos TJ. Goa, a novel gene encoding a ring finger b-box coiled-coil protein, is overexpressed in astrocytoma. Biochem Biophys Res Commun.2001 Aug 24;286(3):574-9.

An FQ, Matsuda M, Fujii H, Tang RF, Amemiya H, Dai YM, Matsumoto Y. Tumor heterogeneity in small hepatocellular carcinoma: analysis of tumor cell proliferation, expression and mutation of p53 AND beta-catenin. Int J Cancer. 2001 Aug 15;93(4):468-74. 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. Proc Natl Acad Sci U S A. 2001 Aug14;98(17):9796-801.

Porter DA, Krop IE, Nasser S, Sgroi D, Kaelin CM, Marks JR, Riggins G, Polyak K. A SAGE (serial analysis of gene expression) view of breast tumor progression. Cancer Res. 2001 Aug1;61(15):5697-702.

Sasaki M, Nakahira K, Kawano Y, Katakura H, Yoshimine T, Shimizu K, Kim SU, Ikenaka K. MAGE-E1, a new member of the melanoma-associated antigen gene family and its expression in human glioma. Cancer Res. 2001 Jun 15;61(12):4809-14. Argani P, Rosty C, Reiter RE, Wilentz RE, Murugesan SR, Leach SD, Ryu B, Skinner HG, Goggins M, Jaffee EM, Yeo CJ, Cameron JL, Kern SE, Hruban RH. Discovery of new markers of cancer through serial analysis of gene expression: prostate stem cell antigen is overexpressed in pancreatic adenocarcinoma. Cancer Res. 2001 Jun 1;61(11):4320-4. Waghray A, Schober M, Feroze F, Yao F, Virgin J, Chen YQ. Identification of prostate cancer. Cancer Res. 2001 May 15;61(10):4283-6.

Yamashita T, Kaneko S, Hashimoto S, Sato T, Nagai S, Toyoda N, Suzuki T, Kobayashi K, Matsushima K. Serial analysis of gene expression in chronic hepatitis C and hepatocellular carcinoma. Biochem Biophys Res Commun. 2001 Mar 30;282(2):647-54. Ikenaka K, Sasaki M, Tamura K, Tamura M, Miyao Y, Nanmoku K, Kawano Y, Nakahira K, Yoshimine T, Shimizu K. Treatment of glioblastoma by direct inoculation of concentrated high titer-recombinant retrovirus carrying the herpes simplex virus thymidine kinase gene. Hum Cell. 2001 Mar;14(1):49-58. Nestl A, Von Stein OD, Zatloukal K, Thies WG, Herrlich P, Hofmann M, Sleeman JP Geneexpression patterns associated with the metastatic phenotype in rodent and humantumors. Cancer Res. 2001 Feb 15;61(4):1569-77.

Hough CD, Sherman-Baust CA, Pizer ES, Montz FJ, Im DD, Rosenshein NB, Cho KR, Riggins GJ, Morin PJ. Large-scale serial analysis of gene expression reveals genes differentially expressed in ovarian cancer. Cancer Res. 2000 Nov15;60(22):6281-7.

Parle-McDermott A, McWilliam P, Tighe O, Dunican D, Croke DT. Serial analysis of gene expression identifies putative metastasis-associated transcripts in colon tumour cell lines. Br J Cancer. 2000 Sep;83(6):725-8

Bahrenberg G, Brauers A, Joost HG, Jakse G. Reduced expression of PSCA, a member of the LY-6 family of cell surface antigens, in bladder, esophagus, and stomach tumors. Biochem Biophys Res Commun. 2000 Sep 7;275(3):783-8

Xu LL, Shanmugam N, Segawa T, Sesterhenn IA, McLeod DG, Moul JW, Srivastava S. A novel androgen-regulated gene, PMEPA1, located on chromosome 20q13 exhibits high level expression in prostate. Genomics. 2000 Jun 15;66(3):257-63

Ryu B, Jones J, Hollingsworth MA, Hruban RH, Kern SE. Invasion-specific genes in malignancy: serial analysis of gene expression comparisons of primary and passaged cancers. Cancer Res. 2001 Mar 1;61(5):1833-8.

Takano T, Amino N. [Molecular-based diagnosis of thyroid carcinomas by detecting cancer-specific mRNAs]. Rinsho Byori. 2000 Feb;48(2):149-54. Review. Japanese

van Limpt V, Chan A, Caron H, Sluis PV, Boon K, Hermus MC, Versteeg R. SAGE analysis of neuroblastoma reveals a high expression of the human homologue of the drosophila delta gene. Med Pediatr Oncol. 2000 Dec;35(6):554-8.

Takano T, Hasegawa Y, Matsuzuka F, Miyauchi A, Yoshida H, Higashiyama T, Kuma K, Amino N Gene expression profiles in thyroid carcinomas. Br J Cancer. 2000 Dec;83(11):1495-502. Nacht M, Ferguson AT, Zhang W, Petroziello JM, Cook BP, Gao YH, Maguire S, Riley D, Coppola G, Landes GM, Madden SL, Sukumar S. Combining serial analysis of gene expression and array technologies to identify genes differentially expressed in breast cancer. Cancer Res 1999 Nov 1;59(21):5464-70

Hibi K, Westra WH, Borges M, Goodman S, Sidransky D, Jen J. PGP9.5 as a candidate tumor marker for non-small-cell lung cancer. Am J Pathol 1999 Sep;155(3):711-5

Hibi K, Liu Q, Beaudry GA, Madden SL, Westra WH, Wehage SL, Yang SC, Heitmiller RF, Bertelsen AH, Sidransky D, Jen J (1998) Serial analysis of gene expression in non-small cell lung cancer. Cancer Res 58:5690-4

Zhang L, Zhou W, Velculescu VE, Kern SE, Hruban RH, Hamilton SR, Vogelstein B, and Kinzler KW (1997). Gene Expression Profiles in Normal and Cancer Cells. Science 276, 1268-1272

Human Disease

Graca L, Thompson S, Lin CY, Adams E, Cobbold SP, Waldmann H. Both CD4(+)CD25(+) and CD4(+)CD25(-) regulatory cells mediate dominant transplantation tolerance. J Immunol. 2002 Jun 1;168(11):5558-65.

Myerowitz R, Lawson D, Mizukami H, Mi Y, Tifft CJ, Proia RL. Molecular pathophysiology in Tay-Sachs and Sandhoff diseases as revealed by gene expression profiling. Hum Mol Genet. 2002 May 15;11(11):1343-50.

Higashi N, Fujioka K, Denda-Nagai K, Hashimoto S, Nagai S, Sato T, Fujita Y, Morikawa A, Tsuiji M, Miyata-Takeuchi M, Sano Y, Suzuki N, Yamamoto K, Matsushima K, Irimura T.

The macrophage C-type lectin specific for galactose/N-acetylgalactosamine is an endocytic receptor expressed on monocyte-derived immature dendritic cells. J Biol Chem. 2002 Jun 7;277(23):20686-93.

Cao W, Mattagajasingh SN, Xu H, Kim K, Fierlbeck W, Deng J, Lowenstein CJ, Ballermann BJ. TIMAP, a novel CAAX box protein regulated by TGF-beta1 and expressed in endothelial cells. Am J Physiol Cell Physiol. 2002 Jul;283(1):C327-37.

Feldhahn N, Schwering I, Lee S, Wartenberg M, Klein F, Wang H, Zhou G, Wang SM, Rowley JD, Hescheler J, Kronke M, Rajewsky K, Kuppers R, Muschen M. Silencing of B cell receptor signals in human naive B cells. J Exp Med. 2002 Nov 18;196(10):1291-305.

Trendelenburg G, Prass K, Priller J, Kapinya K, Polley A, Muselmann C, Ruscher K, Kannbley U, Schmitt AO, Castell S, Wiegand F, Meisel A, Rosenthal A, Dirnagl U.

Serial analysis of gene expression identifies metallothionein-II as major neuroprotective gene in mouse focal cerebral ischemia. J Neurosci. 2002 Jul 15;22(14):5879-88.

Obata-Onai A, Hashimoto S, Onai N, Kurachi M, Nagai S, Shizuno K, Nagahata T, Mathushima K. Comprehensive gene expression analysis of human NK cells and CD8(+) T lymphocytes. Int Immunol. 2002 Oct;14(10):1085-98.

Muschen M, Lee S, Zhou G, Feldhahn N, Barath VS, Chen J, Moers C, Kronke M, Rowley JD, Wang SM. Molecular portraits of B cell lineage commitment. Proc Natl Acad Sci U S A. 2002 Jul 23;99(15):10014-9.

Cao W, Mattagajasingh SN, Xu H, Kim K, Fierlbeck W, Deng J, Lowenstein CJ, Ballermann BJ. TIMAP, a novel CAAX box protein regulated by TGF-beta1 and expressed in endothelial cells. Am J Physiol Cell Physiol. 2002 Jul;283(1):C327-37.

Graca L, Thompson S, Lin CY, Adams E, Cobbold SP, Waldmann H. Both CD4(+)CD25(+)and CD4(+)CD25(-) regulatory cells mediate dominant transplantation tolerance. JImmunol. 2002 Jun 1;168(11):5558-65.

Higashi N, Fujioka K, Denda-Nagai K, Hashimoto S, Nagai S, Sato T, Fujita Y, Morikawa A, Tsuiji M, Miyata-Takeuchi M, Sano Y, Suzuki N, Yamamoto K, Matsushima K, Irimura T.

The Macrophage C-type Lectin Specific for Galactose/N-Acetylgalactosamine Is an Endocytic Receptor Expressed on Monocyte-derived Immature Dendritic Cells. J Biol Chem. 2002 Jun 7;277(23):20686-93.

Myerowitz R, Lawson D, Mizukami H, Mi Y, Tifft CJ, Proia RL. Molecular pathophysiology in Tay-Sachs and Sandhoff diseases as revealed by gene expression profiling. Hum Mol Genet. 2002 May 15;11(11):1343-50.

van Ruissen F, Jansen BJ, de Jongh GJ, Zeeuwen PL, Schalkwijk J. A partial transcriptome of human epidermis. Genomics. 2002 May;79(5):671-8.

Gunnersen JM, Augustine C, Spirkoska V, Kim M, Brown M, Tan SS. Global analysis of gene expression patterns in developing mouse neocortex using serial analysis of gene expression. Mol Cell Neurosci. 2002 Apr;19(4):560-73. Feroze-Merzoug F, Berquin IM, Dey J, Chen YQ. Peptidylprolyl isomerase A (PPIA) as a preferred internal control over GAPDH and beta-actin in quantitative RNA analyses. Biotechniques. 2002 Apr;32(4):776-8, 780, 782.

Schelling JR, El-Meanawy MA, Barathan S, Dodig T, Iyengar SK, Sedor JR. Generation of kidney transcriptomes using serial analysis of gene expression. Exp Nephrol. 2002;10(2):82-92.

Cheng G, Porter JD. Transcriptional profile of rat extraocular muscle by serial analysis of gene expression. Invest Ophthalmol Vis Sci. 2002 Apr;43(4):1048-58.

Anisimov SV, Tarasov KV, Tweedie D, Stern MD, Wobus AM, Boheler KR. SAGE identification of gene transcripts with profiles unique to pluripotent mouse R1 embryonic stem cells. Genomics. 2002

Enerback C, Porter DA, Seth P, Sgroi D, Gaudet J, Weremowicz S, Morton CC, Schnitt S, Pitts RL, Stampl J, Barnhart K, Polyak K. Psoriasin expression in mammary epithelial cells in vitro and in vivo. Cancer Res. 2002 Jan 1;62(1):43-7.

Altered hippocampal gene expression prior to the onset of spontaneous seizures in the rat post-status epilepticus model. Eur J Neurosci. 2001 Nov;14(9):1475-84.

Aronica E, van Vliet EA, Hendriksen E, Troost D, Lopes da Silva FH, Gorter JA. Cystatin C, a cysteine protease inhibitor, is persistently up-regulated in neurons and glia in a rat model for mesial temporal lobe epilepsy. Eur J Neurosci. 2001 Nov;14(9):1485-91.

Monajemi H, Arkenbout EK, Pannekoek H. Gene expression in atherogenesis. Thromb Haemost. 2001 Jul;86(1):404-12. Review.

Datson NA, van der Perk J, de Kloet ER, Vreugdenhil E. Identification of corticosteroid-responsive genes in Shires J, Theodoridis E, Hayday AC. Biological insights into TCRgammadelta+ and TCRalphabeta+Sep;15(3):419-34.

Datson NA, van der Perk J, de Kloet ER, Vreugdenhil E. Expression profile of 30,000 genes in rat hippocampus using SAGE. Hippocampus. 2001;11(4):430-44.

Riggins GJ. Using Serial Analysis of Gene Expression to identify tumor markers and antigens. Dis Markers. 2001;17(2):41-8. Review.

Kuramasu A, Kubota Y, Matsumoto K, Nakajima T, Sun XM, Watanabe T, Saito H, Ohtsu H. Identification of novel mast cell genes by serial analysis of gene expression in cord blood-derived mast cells. FEBS Lett. 2001 Jun 1;498(1):37-41. Peters DG, Kassam AB, Feingold E, Heidrich-O'Hare E, Yonas H, Ferrell RE Brufsky A. Molecular Anatomy of an Intracranial Aneurysm : Coordinated Expression of Genes Involved in Wound Healing and Tissue Remodeling. Stroke. 2001 Apr;32(4):1036-42.

St-Amand J, Okamura K, Matsumoto K, Shimizu S, Sogawa Y Characterization of control and immobilized skeletal muscle: an overview from genetic engineering. FASEB J. 2001 Mar 1;15(3):684-692.

Lee S, Zhou G, Clark T, Chen J, Rowley JD, Wang SM The pattern of gene expression in human CD15+ myeloid progenitor cells. Proc Natl Acad Sci U S A. 2001 Mar 13;98(6):3340-5.

Robert-Nicoud M, Flahaut M, Elalouf JM, Nicod M, Salinas M, Bens M, Doucet A, Wincker P, Artiguenave F, Horisberger JD, Vandewalle A, Rossier BC, Firsov D Transcriptome of a mouse kidney cortical collecting duct cell line: Effects of aldosterone and vasopressin. Proc Natl Acad Sci U S A. 2001 Feb 27;98(5):2712-2716.

Kenzelmann M, Muhlemann K. Transcriptome analysis of fibroblast cells immediate-early after human cytomegalovirus infection. J Mol Biol. 2000 Dec 15;304(5):741-51.

Hashimoto SI, Suzuki T, Nagai S, Yamashita T, Toyoda N, Matsushima K. Identification of genes specifically expressed in human activated and maturedendritic cells through serial analysis of gene expression. Blood. 2000 Sep 15;96(6):2206-14.

Seth A, Lee BK, Qi S, Vary CP. Coordinate expression of novel genes duringosteoblast differentiation. J Bone Miner Res. 2000 Sep;15(9):1683-96

Shklyaev S, Namba H, Hara T, Ohtsuru A, Yamashita S. Sage transcript profiles in cultured human fetal fibroblasts, WI-38. DNA Seq. 2000;11(3-4):281-6.

Inoue H, Sawada M, Ryo A, Tanahashi H, Wakatsuki T, Hada A, Kondoh N, Nakagaki K, Takahashi K, Suzumura A, Yamamoto M, Tabira T. Serial analysis of gene expression in a microglial cell line. Glia 1999 Dec;28(3):265-271

Chen H, Centola M, Altschul SF, Metzger H (1998). Characterization of gene expression in resting and activated mast cells. J Exp Med 188:1657-68

Pathway analysis

Torocsik B, Angelastro JM, Greene LA. The basic region and leucine zipper transcription factor MafK is a new nerve growth factor-responsive immediate early gene that regulates neurite outgrowth. J Neurosci. 2002 Oct 15;22(20):8971-80.

Potapova O, Anisimov SV, Gorospe M, Dougherty RH, Gaarde WA, Boheler KR, Holbrook NJ. Targets of c-Jun NH(2)-terminal kinase 2-mediated tumor growth regulation revealed by serial analysis of gene expression. Cancer Res. 2002 Jun1;62(11):3257-63.

Menssen A, Hermeking H. From the Cover: Characterization of the c-MYC-regulated transcriptome by SAGE: Identification and analysis of c-MYC target genes. Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):6274-9.

Angelastro JM, Torocsik B, Greene LA. Nerve growth factor selectively regulates expression of transcripts encoding ribosomal proteins. BMC Neurosci. 2002;3(1):3.

Clegg N, Eroglu B, Ferguson C, Arnold H, Moorman A, Nelson PS. Digital expression profiles of the prostate androgen-response program. J Steroid Biochem Mol Biol. 2002 Jan;80(1):13-23.

Jasper H, Benes V, Schwager C, Sauer S, Clauder-Munster S, Ansorge W, Bohmann D. The genomic response of the Drosophila embryo to JNK signaling. Dev Cell. 2001 Oct;1(4):579-86.

Boon K, Caron HN, van Asperen R, Valentijn L, Hermus MC, van Sluis P, Roobeek I, Weis I, Voute PA, Schwab M, Versteeg R.N-myc enhances the expression of a large set of genes functioning in ribosome biogenesis and protein synthesis. EMBO J. 2001 Mar 15;20(6):1383-1393.

Charpentier AH, Bednarek AK, Daniel RL, Hawkins KA, Laflin KJ, Gaddis S, MacLeod MC, Aldaz CM. Effects of estrogen on global gene expression: identification of novel targets of estrogen action. Cancer Res. 2000 Nov 1;60(21):5977-83.

Angelastro JM, Klimaschewski L, Tang S, Vitolo OV, Weissman TA, Donlin LT, Shelanski ML, Greene LA. Identification of diverse nerve growthfactor-regulated genes by serial analysis of gene expression (SAGE) profiling. Proc Natl Acad Sci U S A. 2000 Sep 12;97(19):10424-9.

Inadera H, Hashimoto S, Dong HY, Suzuki T, Nagai S, Yamashita T, Toyoda N, Matsushima K. WISP-2 as a novel estrogen-responsive gene in human breast cancer cells. Biochem Biophys Res Commun. 2000 Aug 18;275(1):108-14

Zakin L, Reversade B, Virlon B, Rusniok C, Glaser P, Elalouf JM, Brulet P. Gene expression profiles in normal and Otx2-/- early gastrulating mouseembryos. Proc Natl Acad Sci U S A. 2000 Dec 12

He TC, Chan TA, Vogelstein B, Kinzler KW. PPARdelta is an APC-regulated target of nonsteroidal anti-inflammatory drugs. Cell 1999 Oct 29;99(3):335-45

Hermeking H, Lengauer C, Polyak K, He TC, Zhang L, Thiagalingam S, Kinzler KW, Vogelstein B. (1997) 14-3-3 sigma is a p53-regulated inhibitor of G2/M progression. Mol Cell 1:3-11

Plant and model organisms

Fujii S, Amrein H. Genes expressed in the Drosophila head reveal a role for fat cells in sex-specific physiology. EMBO J. 2002 Oct 15;21(20):5353-63.

Cummings LM, Wirth DF. Serial analysis of gene expression (SAGE) in Plasmodium falciparum: application of the technique to A-T rich genomes. Mol Biochem Parasitol. 2001 Mar;113(1):23-34.

Drawid A, Jansen R, Gerstein M. Genome-wide analysis relating expression level with protein subcellular localization. Trends Genet. 2000 Oct;16(10):426-30

Jansen R, Gerstein M. Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins. Nucleic AcidsRes. 2000 Mar 15;28(6):1481-8.

Futcher B, Latter GI, Monardo P, McLaughlin CS, Garrels JI. A sampling of the yeast proteome. Mol Cell Biol. 1999 Nov;19(11):7357-68.

Basrai MA, Velculescu VE, Kinzler KW, Hieter P. NORF5/HUG1 Is a Component of the MEC1-Mediated Checkpoint Response to DNA Damage and Replication Arrest in Saccharomyces cerevisiae. Mol Cell Biol 1999 Oct;19(10):7041-7049

Kal AJ, van Zonneveld AJ, Benes V, van den Berg M, Koerkamp MG, Albermann K, Strack N, Ruijter JM, Richter A, Dujon B, Ansorge W, Tabak HF. Dynamics of gene expression revealed by comparison of serial analysis of gene expression transcript profiles from yeast grown on two different carbon sources. Mol Biol Cell 1999 Jun;10(6):1859-72

Velculescu, VE, Zhang L, Zhou W, Vogelstein J, Basrai MA, Bassett DE, Hieter P, Vogelstein B, and Kinzler KW (1997). Characterization of the yeast transcriptome. Cell 88, 243-251

Bioinformatics and transcriptome analysis

Ruijter JM, Van Kampen AH, Baas F. Statistical evaluation of SAGE libraries: consequences for experimental design. Physiol Genomics. 2002 Oct 29;11(2):37-44.

Kuznetsov VA, Knott GD, Bonner RF. General statistics of stochastic process of gene expression in eukaryotic cells. Genetics. 2002 Jul;161(3):1321-32.

Oshiro G, Wodicka LM, Washburn MP, Yates JR 3rd, Lockhart DJ, Winzeler EA. Parallel identification of new genes in Saccharomyces cerevisiae. Genome Res. 2002 Aug;12(8):1210-20.

Lercher MJ, Urrutia AO, Hurst LD.Unified model of gene order in the human genome. Nat Genet. 2002 May 6

Lee S, Clark T, Chen J, Zhou G, Scott LR, Rowley JD, Wang SM. Correct identification

of genes from serial analysis of gene expression tag sequences. Genomics. 2002

Apr;79(4):598-602.

Pauws E, van Kampen AH, van de Graaf SA, de Vijlder JJ, Ris-Stalpers C.Nucleic Acids Res. 2001 Apr 15;29(8):1690-4.

Stoeckert C, Pizarro A, Manduchi E, Gibson M, Brunk B, Crabtree J, Schug J,Bioinformatics. 2001 Apr;17(4):300-8.

Angelastro JM, Ryu EJ, Torocsik B, Fiske BK, Greene LA. Blue-white selection step enhances the yield of SAGE concatemers. Biotechniques. 2002 Mar;32(3):484, 486. No abstract available.

Ishii M, Hashimoto Si, Tsutsumi S, Wada Y, Matsushima K, Kodama T, Aburatani H. Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis. Genomics. 2000 Sep 1;68(2):136-43.

Colinge J, Feger G. Detecting the impact of sequencing errors on SAGE data. Bioinformatics. 2001 Sep;17(9):840-2.

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. A public database for gene expression in human cancers. Cancer Res 1999 Nov 1;59(21):5403-7

van Kampen AH, van Schaik BD, Pauws E, Michiels EM, Ruijter JM, Caron HN, Versteeg R, Heisterkamp SH, Leunissen JA, Baas F, van der Mee M USAGE: a web-based approachtowards the analysis of SAGE data. Serial Analysis of Gene Expression. Bioinformatics. 2000Oct;16(10):899-905.

Jansen R, Gerstein M. Analysis of the yeast transcriptome with structural and functional categories: characterizing highly expressed proteins. Nucleic Acids Res. 2000 Mar 15;28(6):1481-8.

Drawid A, Jansen R, Gerstein M. Genome-wide analysis relating expression level with protein subcellular localization. Trends Genet. 2000 Oct;16(10):426-30

Margulies EH, Innis JW. eSAGE: managing and analysing data generated with Serial Analysis of Gene Expression (SAGE). Bioinformatics. 2000Jul;16(7):650-651

Stollberg J, Urschitz J, Urban Z, Boyd CD. A quantitative evaluation of SAGE. Genome Res. 2000 Aug;10(8):1241-8

Lash AE, Tolstoshev CM, Wagner L, Schuler GD, Strausberg RL, Riggins GJ, Altschul SF. SAGEmap: a public gene expression resource. Genome Res. 2000Jul;10(7):1051-60

Larsson M, Stahl S, Uhlen M, Wennborg A. Expression profile viewer (ExProView): a software tool for transcriptome analysis. Genomics. 2000 Feb1;63(3):341-53

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. A public database for gene expression in human cancers. Cancer Res 1999 Nov 1;59(21):5403-7

Technological Advances

Angelastro JM, Ryu EJ, Torocsik B, Fiske BK, Greene LA. Blue-white selection step enhances the yield of SAGE concatemers. Biotechniques. 2002 Mar;32(3):484, 486. No abstract available.

Evans SJ, Datson NA, Kabbaj M, Thompson RC, Vreugdenhil E, De Kloet ER, Watson SJ, Akil H. Evaluation of Affymetrix Gene Chip sensitivity in rat hippocampal tissue using SAGE analysis. Serial Analysis of Gene Expression. Eur J Neurosci. 2002 Aug;16(3):409-13.

Chen J, Sun M, Lee S, Zhou G, Rowley JD, Wang SM. Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc Natl Acad Sci U S A. 2002 Sep 17;99(19):12257-62.

Saha S, Sparks AB, Rago C, Akmaev V, Wang CJ, Vogelstein B, Kinzler KW, 2002 May;20(5):508-12.

Yamamoto M. [Gene expression profiling using improved SAGE]Rinsho Byori. Chen J, Lee S, Zhou G, Wang SM. High-throughput GLGI procedure for converting a large number of serial analysis of gene expression tag sequences into 3' complementary DNAs. Genes Chromosomes Cancer. 2002 Mar;33(3):252-61.

Lee S, Chen J, Zhou G, Wang SM. Generation of high-quantity and quality tag/ditag cDNAs for SAGE analysis. Biotechniques. 2001 Aug;31(2):348-50, 352-4.

St Croix B, Rago C, Velculescu V, Traverso G, Romans KE, Montgomery E, Lal A, Riggins GJ, Lengauer C, Vogelstein B, Kinzler KW. Genes expressed in human tumor endothelium. Science. 2000 Aug 18;289(5482):1197-202.

Angelastro JM, Klimaschewski LP, Vitolo OV. Improved NlaIII digestion of PAGE-purified 102 bp ditags by addition of a single purification step in both the SAGE and microSAGE protocols. Nucleic Acids Res. 2000 Jun 15;28(12):E62

Ye SQ, Zhang LQ, Zheng F, Virgil D and Kwiterovich PO (2000) miniSAGE: gene expression profiling using serial analysis of gene expression from 1 microg total RNA. Anal Biochem. 2000 Dec 1;287(1):144-52.

Caron H, van Schaik B, van der Mee M, Baas F, Riggins G, van Sluis P, Hermus MC, van Asperen R, Boon K, Voûte PA, Heisterkamp S, van Kampen A and Versteeg R (2001). The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains. Science 291, 1289-1292.

van den Berg A, van der Leij J, Poppema S. Serial analysis of gene expression: rapid RT-PCR analysis of unknown SAGE tags. Nucleic Acids Res 1999 Sep 1;27(17):e17

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