Genome-wide expression profiling in Escherichia coli K-12

Nucleic Acids Research

Volumn 27, Issue 19, 1999, Pages 3821-3835

  Richmond, Craig S ^a   Glasner, Jeremy D ^a   Mau, Robert ^a   Jin, Hongfan ^a   Blattner, Frederick R ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; BACTERIAL PROTEIN; COMPLEMENTARY DNA; FLUORESCENT DYE; ISOPROPYL THIOGALACTOSIDE;

ARTICLE; BACTERIAL GENE; DNA HYBRIDIZATION; ESCHERICHIA COLI K 12; GENE AMPLIFICATION; GENE EXPRESSION; GENE SEQUENCE; HEAT SHOCK; NONHUMAN; OPEN READING FRAME; OPERON; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL;

ESCHERICHIA COLI; GENE EXPRESSION PROFILING; GENES, BACTERIAL; GENOME, BACTERIAL; HEAT-SHOCK RESPONSE; ISOPROPYL THIOGALACTOSIDE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; TRANSCRIPTION, GENETIC;

EID: 0033214149     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/27.19.3821     Document Type: Article

References (60)

1. Blattner, F.R., Plunkett, G.III, Bloch, C.A., Perna, N.T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J.D., Rode, C.K., Mayhew, G.F., Gregor, J., Davis, N.W., Kirkpatrick, H.A., Goeden, M.A., Rose, D.J., Mau, B. and Shao, Y. (1997) Science, 277, 1453-1474.
2. Bult, C.J., White, O., Olsen, G.J., Zhou, L., Fleischmann, R.D., Sutton, G.G., Blake, J.A., FitzGerald, L.M., Clayton, R.A., Gocayne, J.D., Kerlavage, A.R., Dougherty, B.A., Tomb, J.F., Adams, M.D., Reich, C.I., Overbeek, R., Kirkness, E.F., Weinstock, K.G., Merrick, J.M., Glodek, A., Scott, J.L., Geoghagen, N.S.M. and Venter, J.C. (1996) Science, 273, 1058-1073.
3. Cole, S.T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S.V., Eiglmeier, K., Gas, S., Barry, C.E.III, Tekaia, F., Badcock, K., Basham, D., Brown, D., Chillingworth, T., Connor, R., Davies, R., Devlin, K., Feltwell, T., Gentles, S., Hamlin, N., Holroyd, S., Hornsby, T., Jagels, K., Barrell, B.G. et al. (1998) Nature, 393, 537-544.
4. Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., Bult, C.J., Tomb, J.F., Dougherty, B.A., Merrick, J.M. et al. (1995) Science, 269, 496-512.
5. Himmelreich, R., Hilbert, H., Plagens, H., Pirkl, E., Li, B.C. and Herrmann, R. (1996) Nucleic Acids Res., 24, 4420-4449.
6. Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G., Azevedo, V., Bertero, M.G., Bessieres, P., Bolotin, A., Borchert, S., Borriss, R., Boursier, L., Brans, A., Braun, M., Brignell, S.C., Bron, S., Brouillet, S., Bruschi, C.V., Caldwell, B., Capuano, V., Carter, N.M., Choi, S.K., Codani, J.J., Connerton, I.F., Danchin, A. et al. (1997) Nature, 390, 249-256.
7. Chuang, S.-E., Daniels., D.L. and Blattner, F.R. (1993) J. Bacteriol., 175, 2026-2036.
8. Shalon, D., Smith, S.J. and Brown, P.O. (1996) Genome Res., 6, 639-645.
9. Schena, M., Shalon, D., Davis, R.W. and Brown, P.O. (1995) Science, 270, 467-470.
10. Welford, S.M., Gregg, J., Chen, E., Garrison, D., Sorensen, P.H., Denny, C.T. and Nelson, S.F. (1998) Nucleic Acids Res., 26, 3059-3065.
11. Khan, J., Simon, R., Bittner, M., Chen, Y., Leighton, S.B., Pohida, T., Smith, P.D., Jiang, Y., Gooden, G.C., Trent, J.M. and Meltzer, P.S. (1998) Cancer Res., 58, 5009-5013.
12. DeRisi, J.L., Iyer, V.R. and Brown, P.O. (1997) Science, 278, 680-686.
13. Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botstein, D., Brown, P.O. and Herskowitz, I. (1998) Science, 282, 699-705.
14. Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P.O. and Davis, R.W. (1996) Proc. Natl Acad. Sci. USA, 93, 10614-10619.
15. Zhu, H., Cong, J.P., Mamtora, G., Gingeras, T. and Shenk, T. (1998) Proc. Natl Acad. Sci. USA, 95, 14470-14475.
16. Wodicka, L., Dong, H., Mittmann, M., Ho, M.H. and Lockhart, D.J. (1997) Nature Biotechnol., 15, 1359-1367.
17. Holstege, F.C., Jennings, E.G., Wyrick, J.J., Lee, T.I., Hengartner, C.J., Green, M.R., Golub, T.R., Lander, E.S. and Young, R.A. (1998) Cell, 95, 717-728.
18. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botstein, D. and Futcher, B. (1998) Mol. Biol. Cell, 9, 3273-3297.
19. Gingeras, T.R., Ghandour, G., Wang, E., Berno, A., Small, P.M., Drobniewski, F., Alland, D., Desmond, E., Holodniy, M. and Drenkow, J. (1998) Genome Res., 8, 435-448.
20. Behr, M.A., Wilson, M.A., Gill, W.P., Salamon, H., Schoolnik, G.K., Rane, S. and Small, P.M. (1999) Science, 284, 1520-1523.
21. Iyer, V.R., Eisen, M.B., Ross, D.T., Schuler, G., Moore, T., Lee, J.C.F., Trent, J.M., Staudt, L.M., Hudson, J.Jr, Boguski, M.S., Lashkari, D., Shalon, D., Botstein, D. and Brown, P.O. (1999) Science, 283, 83-87.
22. Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Proc. Natl Acad. Sci. USA, 95, 14863-14868.
23. Neidhardt, F.C., Bloch, P.L. and Smith, D.F. (1974) J. Bacteriol., 119, 736-747.
24. Sambrook, J., Fritsch, E.F. and Maniatis, T. (eds), (1989) Molecular Cloning: A Laboratory Manual. 2nd Edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY.
25. Andre, P., Kim, A., Khrapko, K. and Thilly, W.G. (1997) Genome Res., 7, 843-852.
26. Lundberg, K.S., Shoemaker, D.D., Adams, M.W., Short, J.M., Sorge, J.A. and Mathur, E.J. (1991) Gene, 108, 1-6.
27. Cline, J., Braman, J.C. and Hogrefe, H.H. (1996) Nucleic Acids Res., 24, 3546-3551.
28. Barnes, W.M. (1994) Proc. Natl Acad. Sci. USA, 91, 2216-2220.
29. Webster, C., Kempsell, K., Booth, I. and Busby, S. (1987) Gene, 59, 253-263.
30. Miller, J.H. (1980) In Miller, J.H. and Reznikoff, W.S. (eds), The Operon. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, pp. 31-88.
31. Stokes, H.W. and Hall, B.G. (1985) Mol. Biol. Evol., 2, 478-483.
32. Wilbur, W.J. and Lipman, D.J. (1983) Proc. Natl Acad. Sci. USA, 80, 726-730.
33. Heller, R.A., Schena, M., Chai, A., Shalon, D., Bedilion, T., Gilmore, J., Woolley, D.E. and Davis, R.W. (1997) Proc. Natl Acad. Sci. USA, 94, 2150-2155.
34. Chuang, S.-E. and Blattner, F.R. (1993) J. Bacteriol., 175, 5242-5252.
35. Gross, C.A. (1996) In Neidhardt, F.C., Curtiss, R.III, Ingraham, J.L., Lin, E.C.C., Low, K.B., Magasanik, B., Reznikoff, W.S., Riley, M., Schaechter, M. and Umbarger, H.E. (eds), Escherichia coli and Salmonella Cellular and Molecular Biology. 2nd Edn. ASM Press, Washington, DC, Vol. 1, pp. 1382-1400.
36. Neidhardt, F.C., VanBogelen, R.A. and Vaughn, V. (1984) Annu. Rev. Genet., 18, 295-329.
37. Neidhardt, F.C. (1987) Genes Dev., 1, 109-110.
38. Lindquist, S. (1986) Annu. Rev. Biochem., 55, 1151-1191.
39. Lemaux, P.G., Herendeen, S.L., Bloch, P.L. and Neidhardt, F.C. (1978) Cell, 13, 427-434.
40. Yamamori, T., Ito, K., Nakamura, Y. and Yura, T. (1978) J. Bacteriol., 134, 1133-1140.
41. Herendeen, S.L., VanBogelen, R.A. and Neidhardt, F.C. (1979) J. Bacteriol., 139, 185-194.
42. Grossman, A.D., Erickson, J.W. and Gross, C.A. (1984) Cell, 38, 383-390.
43. Erickson, J.W. and Gross, C.A. (1989) Genes Dev., 3, 1462-1471.
44. Wang, Q.P. and Kaguni, J.M. (1989) J. Bacteriol., 171, 4248-4253.
45. Watson, N., Dunyak, D.S., Rosey, E.L., Slonczewski, J.L. and Olson, E.R. (1992) J. Bacteriol., 174, 530-540.
46. Yamanaka, K. and Inouye, M. (1997) J. Bacteriol., 179, 5126-5130.
47. Missiakas, D., Mayer, M.P., Lemaire, M., Georgopoulos, C. and Raina, S. (1997) Mol. Microbiol., 24, 355-371.
48. De Las Penas, A., Connolly, L. and Gross, C.A. (1997) Mol. Microbiol., 24, 373-385.
49. Katayama, Y., Gottesman, S., Pumphrey, J., Rudikoff, S., Clark, W.P. and Maurizi, M.R. (1988) J. Biol. Chem., 263, 15226-15236.
50. Gottesman, S., Clark, W.P. and Maurizi, M.R. (1990) J. Biol. Chem., 265, 7886-7893.
51. Kroh, H.E. and Simon, L.D. (1990) J. Bacteriol., 172, 6026-6034.
52. Conlin, C.A., Trun, N.J., Silhavy, T.J. and Miller, C.G. (1992) J. Bacteriol., 174, 5881-5887.
53. Jiang, X., Zhang, M., Ding, Y., Yao, J., Chen, H., Zhu, D. and Muramatu, M. (1998) J. Biochem. (Tokyo), 124, 980-985.
54. Tsui, H.C., Feng, G. and Winkler, M.E. (1996) J. Bacteriol., 178, 5719-5731.
55. Herman, C., Thevenet, D., D'Ari, R. and Bouloc, P. (1995) Proc. Natl Acad. Sci. USA, 92, 3516-3520.
56. Missiakas, D., Schwager, F., Betton, J.M., Georgopoulos, C. and Raina, S. (1996) EMBO J., 15, 6899-6909.
57. Hall, B.G. and Clarke, N.D. (1977) Genetics, 85, 193-201.
58. Gold, L. (1988) Annu. Rev. Biochem., 57, 199-233.
59. Henry, M.D., Yancey, S.D. and Kushner, S.R. (1992) J. Bacteriol., 174, 743-748.
60. Riley, M. (1998) Nucleic Acids Res., 26, 54.