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

Scott HS, Chrast R. Global transcript expression profiling by Serial Analysis of Gene Expression. Genet Eng (N Y). 2001;23:201-19. Review.

Powell J. SAGE. The serial analysis of gene expression. Methods Mol Biol. 2000;99:297-319

Madden SL, Wang CJ, Landes G. Serial analysis of gene expression: from gene discovery to target identification. Drug Discov Today. 2000 Sep;5(9):415-425

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.

Gunnersen JM, Spirkoska V, Smith PE, Danks RA, Tan SS. Growth and migration markers of rat C6 glioma cells identified by serial analysis of gene expression. Glia. 2000 Nov;32(2):146-54

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

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

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

Ferguson AT, Evron E, Umbricht CB, Pandita TK, Chan TA, Hermeking H, Marks JR, Lambers AR, Futreal PA, Stampfer MR, Sukumar S. High frequency of hypermethylation at the 14-3-3 sigma locus leads to gene silencing in breast cancer. Proc Natl Acad Sci U S A. 2000 May 23;97(11):6049-54

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

Michiels E, Oussoren E, Van Groenigen M, Pauws E, Bossuyt PMM, Voûte PA, Baas F. Genes differentially expressed in medulloblastoma and fetal brain. Physiol. Genomics 1: 83-91, 1999

van den Berg A, Visser L, Poppema S. High expression of the CC chemokine TARC in Reed-Sternberg cells. A possible explanation for the characteristic T-cell infiltratein Hodgkin's lymphoma. Am J Pathol 1999 Jun;154(6):1685-91

Michiels EM, Oussoren E, Van Groenigen M, Pauws E, Bossuyt PM, Voute PA, Baas F. Genes differentially expressed in medulloblastoma and fetal brain. Physiol Genomics. 1999 Aug 31;1(2):83-91

Zhou W, Sokoll LJ, Bruzek DJ, Zhang L, Velculescu VE, Goldin SB, Hruban RH, Kern SE, Hamilton SR, Chan DW, Vogelstein B, Kinzler KW. Identifying markers for pancreatic cancer by gene expression analysis. Cancer Epidemiol Biomarkers Prev 1998 Feb;7(2):109-12

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.

Eichenlaub-Ritter U, Peschke M. Expression in in-vivo and in-vitro growing and maturing oocytes: focus on regulation of expression at the translational level. Hum Reprod Update. 2002 Jan-Feb;8(1):21-41.

Welle S. Gene transcript profiling in aging research. Exp Gerontol. 2002 Apr;37(4):583-90.

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.

Sharon D, Blackshaw S, Cepko CL, Dryja TP. Profile of the genes expressed in the human peripheral retina, macula, and retinal pigment epithelium determined through serial analysis of gene expression (SAGE). Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):315-20.

Stanton JL, Bascand M, Fisher L, Quinn M, Macgregor A, Green DP. Gene expression profiling of human GV oocytes: an analysis of a profile obtained by Serial Analysis of Gene Expression (SAGE). J Reprod Immunol. 2002 Jan;53(1-2):193-201.

Vreugdenhil E, de Kloet ER, Schaaf M, Datson NA. Genetic dissection of corticosterone receptor function in the rat hippocampus. Eur Neuropsychopharmacol. 2001 Dec;11(6):423-30.

Hendriksen H, Datson NA, Ghijsen WE, van Vliet EA, da Silva FH, Gorter JA, Vreugdenhil E.

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.

Blackshaw S, Fraioli RE, Furukawa T, Cepko CL. Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes. Cell. 2001 Nov 30;107(5):579-89.

Zhou G, Chen J, Lee S, Clark T, Rowley JD, Wang SM. The pattern of gene expression in human CD34(+) stem/progenitor cells. Proc Natl Acad Sci U S A. 2001 Nov 20;98(24):13966-71.

Chen J, Rowley DA, Clark T, Lee S, Zhou G, Beck C, Rowley JD, Wang SM. The pattern of gene expression in mouse Gr-1(+) myeloid progenitor cells. Genomics. 2001 Oct;77(3):149-62.

Uchida T, Nakao A, Nakano N, Kuramasu A, Saito H, Okumura K, Ra C, Ogawa H. Identification of Nash1, a novel protein containing a nuclear localization signal, a sterile alpha motif, and an SH3 domain preferentially expressed in mast cells. Biochem Biophys Res Commun. 2001 Oct 19;288(1):137-41. Sun Y, Zhang L, Johnston NL, Torrey EF, Yolken RH. Serial analysis of gene expression in the frontal cortex of patients with bipolar disorder. Br J Psychiatry Suppl.2001 Jun;41:s137-41.

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.

Jansen BJ, van Ruissen F, de Jongh G, Zeeuwen PL, Schalkwijk J

Serial analysis of gene expression in differentiated cultures of human epidermal keratinocytes. J Invest Dermatol. 2001 Jan;116(1):12-22.

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

El-Meanawy MA, Schelling JR, Pozuelo F, Churpek MM, Ficker EK, Iyengar S, Sedor JR. Use of serial analysis of gene expression to generate kidneyexpression libraries. Am J Physiol Renal Physiol. 2000 Aug;279(2):F383-92

Welle S, Bhatt K, Thornton CA. High-abundance mRNAs in human muscle: comparisonbetween young and old. J Appl Physiol. 2000 Jul;89(1):297-304

Pauws E, Moreno JC, Tijssen M, Baas F, de Vijlder JJ, Ris-Stalpers C. Serial analysis of gene expression as a tool to assess the human thyroid expression profile and to identify novel thyroidal genes. J Clin Endocrinol Metab. 2000 May;85(5):1923-7

Yamashita T, Hashimoto S, Kaneko S, Nagai S, Toyoda N, Suzuki T, Kobayashi K, Matsushima K. Comprehensive gene expression profile of a normal human liver. Biochem Biophys Res Commun. 2000 Mar 5;269(1):110-6

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

Ryo A, Suzuki Y, Ichiyama K, Wakatsuki T, Kondoh N, Hada A, Yamamoto M, Yamamoto N. Serial analysis of gene expression in HIV-1-infected T cell lines. FEBS Lett 1999 Nov 26;462(1-2):182-186

Hashimoto S, Suzuki T, Dong HY, Yamazaki N, Matsushima K. Serial analysis of gene expression in human monocytes and macrophages. Blood 1999 Aug 1; 94(3):845-52

Welle S, Bhatt K, Thornton CA. Inventory of high-abundance mRNAs in skeletal muscle of normal men. Genome Res 1999 May;9(5):506-13

Virlon B, Cheval L, Buhler JM, Billon E, Doucet A and Elalouf JM (1999). Serial microanalysis of renal transcriptomes. Proc. Natl. Acad. Sci. U S A Dec 21;96(26):15286-91

de Waard V, van den Berg BM, Veken J, Schultz-Heienbrok R, Pannekoek H, van Zonneveld AJ (1999). Serial analysis of gene expression to assess the endothelial cell response to an atherogenic stimulus. Gene 226:1-8

Gonzalez-Zulueta M, Ensz LM, Mukhina G, Lebovitz RM, Zwacka RM, Engelhardt JF, Oberley LW, Dawson VL, Dawson TM. Manganese superoxide dismutase protects nNOS neurons from NMDA and nitric oxide-mediated neurotoxicity. J Neurosci 1998 Mar 15;18(6):2040-55

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.

Godfried MB, Veenstra M, v Sluis P, Boon K, v Asperen R, Hermus MC, v Schaik BD, Oncogene. 2002 Mar 27;21(13):2097-101.

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.

Seth P, Krop I, Porter D, Polyak K. Novel estrogen and tamoxifen induced genes identified by SAGE (Serial Analysis of Gene Expression). Oncogene. 2002 Jan 24;21(5):836-43.

Jiang C, Lu H, Vincent KA, Shankara S, Belanger AJ, Cheng SH, Akita GY, Kelly RA, Goldberg MA, Gregory RJ. Gene expression profiles in human cardiac cells subjected to hypoxia or expressing a hybrid form of HIF-1 alpha. Physiol Genomics. 2002 Feb 11;8(1):23-32.

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.

Suzuki T, Hashimoto Si, Toyoda N, Nagai S, Yamazaki N, Dong HY, Sakai J, Yamashita T, Nukiwa T, Matsushima K. Comprehensive gene expression profile of LPS-stimulated human monocytes by SAGE. Blood. 2000 Oct 1;96(7):2584-91

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

Ji X, Chen D, Xu C, Harris SE, Mundy GR, Yoneda T. Patterns of gene expression associated with BMP-2-induced osteoblast and adipocyte differentiation of mesenchymal progenitor cell 3T3-F442A. J Bone Miner Metab. 2000;18(3):132-9

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

He TC, Sparks AB, Rago C, Hermeking H, Zawel L, da Costa LT, Morin PJ, Vogelstein B, Kinzler KW (1998). Identification of c-MYC as a target of the APC pathway. Science 5382:1509-12

Madden SL, Galella EA, Zhu J, Bertelsen AH, and Beaudry GA (1997). SAGE transcript profiles for p53-dependent growth regulation. Oncogene 15, 1079-1085

Polyak K, Xia Y, Zweier JL, Kinzler KW, and Vogelstein B (1997). A model for p53 induced apoptosis. Nature 389, 300-305

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.

Steen BR, Lian T, Zuyderduyn S, MacDonald WK, Marra M, Jones SJ, Kronstad JW. Temperature-Regulated Transcription in the Pathogenic Fungus Cryptococcus neoformans. Genome Res. 2002 Sep;12(9):1386-400.

Lorenz WW, Dean JF. SAGE Profiling and demonstration of differential gene expression along the axial developmental gradient of lignifying xylem in loblolly pine (Pinus taeda). Tree Physiol. 2002 Apr;22(5):301-10.

Logan M. SAGE profiling of the forelimb and hindlimb. Genome Biol. 2002;3(3):REVIEWS1007.

Bahl A, Brunk B, Coppel RL, Crabtree J, Diskin SJ, Fraunholz MJ, Grant GR, Gupta D, Huestis RL, Kissinger JC, Labo P, Li L, McWeeney SK, Milgram AJ, Roos DS, Schug J, Stoeckert CJ Jr. PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished). Nucleic Acids Res. 2002 Jan 1;30(1):87-90.

Patankar S, Munasinghe A, Shoaibi A, Cummings LM, Wirth DF. Serial analysis of gene expression in Plasmodium falciparum reveals the global expression profile of erythrocytic stages and the presence of anti-sense transcripts in the malarial parasite. Mol Biol Cell. 2001 Oct;12(10):3114-25.

Margulies EH, Kardia SL, Innis JW. Identification and prevention of a GC content bias in SAGE libraries. Nucleic Acids Res. 2001 Jun 15;29(12):E60-0.

Jones SJ, Riddle DL, Pouzyrev AT, Velculescu VE, Hillier L, Eddy SR, Stricklin SL, Baillie DL, Waterston R, Marra MA. Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans. Genome Res. 2001 Aug;11(8):1346-52.

Johnson TE. SAGE thoughts on aging. Genome Res. 2001 Aug;11(8):1323-4. No abstract available. Munasinghe A, Patankar S, Cook BP, Madden SL, Martin RK, Kyle DE, Shoaibi A,

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

Matsumura H, Nirasawa S, and Terauchi R (1999). Technical advance: transcript profiling in rice (Oryza sativa L.) seedlings using serial analysis of gene expression. Plant Journal 20(6) 719-726

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

Moreno JC, Pauws E, van Kampen AH, Jedlickova M, de Vijlder JJ, Ris-Stalpers C. Cloning of tissue-specific genes using serial analysis of gene expression and a novel computational substraction approach. Genomics. 2001 Jul;75(1-3):70-6.

Margulies EH, Kardia SL, Innis JW. Identification and prevention of a GC content bias in SAGE libraries. Nucleic Acids Res. 2001 Jun 15;29(12):E60-0. Yamamoto M, Wakatsuki T, Hada A, Ryo A. Use of serial analysis of gene expression (SAGE) technology. J Immunol Methods. 2001 Apr 1; 250(1-2):45-66

Neilson L, Andalibi A, Kang D, Coutifaris C, Strauss JF 3rd, Stanton JA, Green DP. Molecular phenotype of the human oocyte by PCR-SAGE. Genomics. 2000 Jan 1;63(1):13-24

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

Peters DG, Kassam AB, Yonas H, O'Hare EH, Ferrell RE, Brufsky AM. Comprehensive transcript analysis in small quantities of mRNA by SAGE-Lite. Nucleic Acids Res 1999 Dec 15;27(24):e39

Datson NA, van der Perk-de Jong J, van den Berg MP, de Kloet ER, Vreugdenhil E. MicroSAGE: a modified procedure for serial analysis of gene expression in limited amounts of tissue (1999). Nucleic Acids Res 27:1300-1307

Virlon B, Cheval L, Buhler JM, Billon E, Doucet A and Elalouf JM (1999). Serial microanalysis of renal transcriptomes. Proc. Natl. Acad. Sci. U S A Dec 21;96(26):15286-91 Kenzelmann M, Muhlemann K. Substantially enhanced cloning efficiency of SAGE (Serial Analysis of Gene Expression) by adding a heating step to the original protocol (1999). Nucleic Acids Res 27:917-8

Powell J (1998). Enhanced concatemer cloning-a modification to the SAGE (Serial Analysis of Gene Expression) technique. Nucleic Acids Res 26: 3445-6

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