Expression profiling: DNA arrays in many guises

BioEssays

Volumn 21, Issue 9, 1999, Pages 781-790

  Granjeaud, Samuel ^a   Bertucci, François ^b   Jordan, Bertrand R ^a,c  

^a INSERM   (France)

^b INSTITUT PAOLI CALMETTES   (France)

^c CENTRE D IMMUNOLOGIE DE MARSEILLE LUMINY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA ARRAY; GENE EXPRESSION; NUCLEOTIDE SEQUENCE;

DNA; GENE EXPRESSION; GENOME; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 0033200398     PISSN: 02659247     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1521-1878(199909)21:9<781::AID-BIES10>3.0.CO;2-2     Document Type: Article

References (44)

1. Rossi DL, Vicari AP, Franz-Bacon K, McClanahan TK, Zlotnik A. Identification through bioinformatics of two new macrophage proinflammatory human chemokines: MIP-3alpha and MIP-3beta. J Immunol 1997;158: 1033-1036.
2. Oettgen P, Alani RM, Barcinski MA, Brown L, Akbarali Y, Boltax J, Kunsch C, Munger K, Libermann TA. Isolation and characterization of a novel epithelium-specific transcription factor, ESE-1, a member of the ets family. Mol Cell Biol 1997;17:4419-4433.
3. Marshall A. HGS launches "first" genomics product in clinic. Nat Biotechnol 1998;16:129.
4. Stipp D. Gene chip breakthrough. Fortune Magazine. March 31, 1997. p 56-73.
5. Nguyen C, Rocha D, Granjeaud S, Baldit M, Bernard K, Naquet P, Jordan BR. Differential gene expression in the murine thymus assayed by quantitative hybridization of arrayed cDNA clones. Genomics 1995;29:207-216.
6. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 1995;270:467-470.
7. Lockhart DJ, Dong H, Byrne MC, Follettie MT, Gallo MV, Chee MS, Mittmann M, Wang C, Kobayashi M, Horton H, Brown EL. Expression monitoring by hybridization to high-density oligonucleotide arrays (see comments). Nat Biotechnol 1996;14:1675-1680.
8. Bernard K, Auphan N, Granjeaud S, Victorero G, Schmitt-Verhulst AM, Jordan BR, Nguyen C. Multiplex messenger assay: simultaneous, quantitative measurement of expression of many genes in the context of T cell activation. Nucleic Acids Res 1996;24:1435-1442.
9. Gress TM, Hoheisel JD, Lennon GG, Zehetner G, Lehrach H. Hybridization fingerprinting of high-density cDNA-library arrays with cDNA pools derived from whole tissues. Mamm Genome 1992;3:609-619.
10. Zhao N, Hashida H, Takahashi N, Misumi Y, Sakaki Y. High-density cDNA filter analysis: a novel approach for large-scale, quantitative analysis of gene expression. Gene 1995;156:207-213.
11. Pietu G, Alibert O, Guichard V, Lamy B, Bois F, Leroy E, Mariage-Sampson R, Houlgatte R, Soularue P, Auffray C. Novel gene transcripts preferentially expressed in human muscles revealed by quantitative hybridization of a high density cDNA array Genome Res 1996;6:492-503.
12. Clontech "ATLAS array." Available at: http://www.clontech.com/clontech/ Catalog/Hybridization/Atlas.html
13. Genome Systems "Gene discovery array." Available at: http://www. genomesystems.com/GDA/
14. Research Genetics "GeneFilters." Available at: http://www.resgen.com/ online_catalog/
15. Chen JJ, Wu R, Yang PC, Huang JY, Sher YP, Han MH, Kao WC, Lee PJ, Chiu TF, Chang F, Chu YW, Wu CW, Peck K. Profiling expression patterns and isolating differentially expressed genes by cDNA microarray system with colorimetry detection. Genomics 1998;51:313-324.
16. Bertucci F, Bernard K, Loriod B, Chang YC, Granjeaud S, Birnbaum D, Nguyen C, Peck K, Jordan BR. Sensitivity issues in DNA array-based expression measurements: advantages of Nylon membranes. Hum Mol Genet 1999 (in press).
17. Schena M, Shalon D, Heller R, Chai A, Brown PO, Davis RW. Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc Natl Acad Sci USA 1996;93:10614-10619.
18. DeRisi JL, Iyer VR, Brown PO. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997;278:680-686.
19. Weinstein JN, Myers TG, PM OC, Friend SH, Fornace AJ Jr, Kohn KW, Fojo T, Bates SE, Rubinstein LV, Anderson NL, Buolamwini JK, van Osdol WW, Monks AP, Scudiero DA, Sausville EA, Zaharevitz DW, Bunow B, Viswanadhan VN, Johnson GS, Wittes RE, Paull KD. An information-intensive approach to the molecular pharmacology of cancer. Science 1997;275:343-349.
20. Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM. Expression profiling using cDNA microarrays. Nat Genet 1999;21:10-14.
21. Bowtell DD. Options available - from start to finish - for obtaining expression data by microarray. Nat Genet 1999;21:25-32.
22. Fodor SP, Read JL, Pirrung MC, Stryer L, Lu AT, Solas D. Light-directed, spatially addressable parallel chemical synthesis. Science 1991;251:767-773.
23. Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ. High density synthetic oligonucleotide arrays. Nat Genet 1999;21:20-24.
24. Affymetrix. Available at: http://www.affymetrix.com/
25. Wodicka L, Dong H, Mittmann M, Ho MH, Lockhart DJ. Genome-wide expression monitoring in Saccharomyces cerevisiae. Nat Biotechnol 1997;15:1359-1367.
26. Cheng J, Sheldon EL, Wu L, Uribe A, Gerrue LO, Carrino J, Heller MJ, O'Connell JP. Preparation and hybridization analysis of DNA/RNA from E. coli on microfabricated bioelectronic chips. Nat Biotechnol 1998;16:541-546.
27. Boguski MS, Schuler GD. ESTablishing a human transcript map. Nat Genet 1995;10:369-371.
28. Genometrix. Available at: http://www.genometrix.com/
29. IMAGE consortium. Available at: http://www-bio.llnl.gov/bbrp/image/ image.html
30. Construction instructions. Available at: http://cmgm.Stanford.edu/pbrown/
31. Genetic Microsystems. Available at: http://www.genomesystems.com/
32. Cartesian. Available at: http://www.cartesiantech.com/
33. BioRobotics. Available at: http://www.biorobotics.com/
34. Molecular Dynamics. Available at: http://www.mdyn.com/
35. General Scanning. Available at: http://www.genscan.com/
36. Granjeaud S, Nguyen C, Rocha D, Luton R, Jordan BR. From hybridization image to numerical values: a practical, high throughput quantification system for high density filter hybridizations. Genet Anal 1996;12:151-162.
37. Bassett DE Jr, Eisen MB, Boguski MS. Gene expression informatics: it's all in your mind. Nat Genet 1999;21:51-55.
38. Imbert MC, Nguyen VK, Granjeaud S, Nguyen C, Jordan BR. "LABNOTE," a laboratory notebook system designed for academic genomics groups. Nucleic Acids Res 1999;27:601-607.
39. Ermolaeva O, Rastogi M, Pruitt KD, Schuler GD, Bittner ML, Chen Y, Simon R, Meltzer P, Trent JM, Boguski MS. Data management and analysis for gene expression arrays. Nat Genet 1998;20:19-23.
40. Chu S, DeRisi J, Eisen M, Mulholland J, Botstein D, Brown PO, Herskowitz I. The transcriptional program of sporulation in budding yeast. Science 1998;282:699-705.
41. Marton MJ, DeRisi JL, Bennett HA, Iyer VR, Meyer MR, Roberts CJ, Stoughton R, Burchard J, Slade D, Dai H, Bassett DE Jr, Hartwell LH, Brown PO, Friend SH. Drug target validation and identification of secondary drug target effects using DNA microarrays. Nat Med 1998;4:1293-1301.
42. Persidis A. Biochips. Nat Biotechnol 1998;16:981-983.
43. Ferguson JA, Boles TC, Adams CP, Walt DR. A fiber-optic DNA biosensor microarray for the analysis of gene expression. Nat Biotechnol 1996;14: 1681-1684.
44. GeSim. Available at: http://www.gesim.de/