Computational methods for the identification of differential and coordinated gene expression

Human Molecular Genetics

Volumn 8, Issue 10, 1999, Pages 1821-1832

  Claverie, Jean Michel ^a  

^a CNRS Aix Marseille University   (France)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY DNA;

DNA TRANSCRIPTION; EXON; GENE EXPRESSION; GENE FUNCTION; GENE SEQUENCE; HUMAN; PRIORITY JOURNAL; PROMOTER REGION; REVIEW; TWO DIMENSIONAL GEL ELECTROPHORESIS; VERTEBRATE;

ANIMALS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENES; GENOME, HUMAN; HUMANS;

EID: 0032837252     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/8.10.1821     Document Type: Review

References (109)

1. The C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science, 282, 2012-2018.
2. Dickson, D. (1998) Drosophila set for fast-track sequencing. Nature, 393, 296.
3. Ecker, J.R. (1998) Genome sequencing: genes blossom from a weed. Nature, 391, 438-439.
4. Wadman, M. (1999) Human genome project aims to finish 'working draft' next year. Nature, 398, 177.
5. Claverie, J.-M. (1997) Computational methods for the identification of genes in vertebrate genomic sequences. Hum. Mol. Genet., 6, 1735-1744.
6. Werner, T. (1999) Models for prediction and recognition of eukaryotic promoters. Mamm. Genome, 10, 168-175.
7. Audic, S. and Claverie, J.-M. (1998) Visualizing the competitive recognition of TATA-boxes in vertebrate promoters. Trends Genet., 14, 10-11.
8. Fickett, J.W. and Hatzigeorgiou, A.G. (1997) Eukaryotic promoter recognition. Genome Res., 7, 861-878.
9. Hofmann, K., Bucher, P., Falquet, L. and Bairoch, A. (1999) The PROSITE database, its status in 1999. Nucleic Acids Res., 27, 215-219.
10. Corpet, F., Gouzy, J. and Kahn, D. (1999) Recent improvements of the ProDom database of protein domain families. Nucleic Acids Res., 27, 263-267.
11. Attwood, T.K., Flower, D.R., Lewis, A.P., Mabey, J.E., Morgan, S.R., Scordis, P., Selley, J.N. and Wright, W. (1999) PRINTS prepares for the new millennium. Nucleic Acids Res., 27, 220-225.
12. Ponting, C.P., Schultz, J., Milpetz, F. and Bork, P. (1999) SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res., 27, 229-232.
13. Bateman, A., Birney, E., Durbin, R., Eddy, S.R., Finn, R.D. and Sonnhammer, E.L. (1999) Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res., 27, 260-262.
14. Henikoff, J.G., Henikoff, S. and Pietrokovski, S. (1999) New features of the Blocks Database servers. Nucleic Acids Res., 27, 226-228.
15. Liang, P. and Pardee, A.B. (1992) Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science, 257, 967-971.
16. Liang, P. and Pardee, A.B. (1998) Differential display. A general protocol. Mol. Biotechnol., 10, 261-267.
17. Okubo, K., Hori, N., Matoba, R., Niiyama, T., Fukushima, A., Kojima, Y. and Matsubara, K. (1992) Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression. Nature Genet., 2, 173-179.
18. Adams, M., Dubnick, M., Kerlavage, A., Moreno, R., Kelley, J., Utterback, T., Nagle, J., Fields, C. and Venter, J. (1992) Sequence identification of 2 375 human brain genes. Nature, 355, 632-634.
19. Matsubara, K. and Okubo, K. (1993) Identification of new genes by systematic analysis of cDNAs and database construction. Curr. Opin. Biotechnol. 4, 672-677.
20. Lee, N.H., Weinstock, K.G., Kirkness, E.F., Earle-Hughes, J.A., Fuldner, R.A., Marmaros, S., Glodek, A., Gocayne, J.D., Adams, M.D., Kerlavage, A.R. et al. (1995) Comparative expressed-sequence-tag analysis of differential gene expression profiles in PC-12 cells before and after nerve growth factor treatment. Proc. Natl Acad. Sci. USA, 92, 8303-8307.
21. Adams, M.D., Kerlavage, A.R., Fleischmann, R.D., Fuldner, R.A., Bult, C.J., Lee, N.H., Kirkness, E.F., Weinstock, K.G., Gocayne, J.D., White, O. et al. (1995) Initial assessment of human gene diversity and expression patterns based upon 83 million nucleotides of cDNA sequence. Nature, 377 (suppl. 6547), 3-174.
22. Aaronson, J., Eckman, B., Blevins, R., Borkowski, J., Myerson, J., Imran, S. and Elliston, K. (1996) Toward the development of a gene index to the human genome: an assessment of the nature of high-throughput EST sequence data. Genome Res., 6, 829-845.
23. Hillier, L.D., Lennon, G., Becker, M., Bonaldo, M.F., Chiapelli, B., Chissoe, S., Dietrich, N., DuBuque, T., Favello, A., Gish, W., Hawkins, M., Hultman, M., Kucaba, T., Lacy, M., Le, M., Le, N., Mardis, E., Moore, B., Morris, M., Parsons, J., Prange, C., Rifkin, L., Rohlfing, T., Schellenberg, K., Marra, M. et al. (1996) Generation and analysis of 280 000 human expressed sequence tags. Genome Res., 6, 807-828.
24. Velculescu, V.E., Zhang, L., Vogelstein, B. and Kinzler, K.W. (1995) Serial analysis of gene expression. Science, 270, 484-487.
25. Ryo, A., Kondoh, N., Wakatsuki, T., Hada, A., Yamamoto, N. and Yamamoto, M. (1998) A method for analyzing the qualitative and quantitative aspects of gene expression: a transcriptional profile revealed for HeLa cells. Nucleic Acids Res., 26, 2586-2592.
26. Datson, N.A., van der Perk-de Jong, J., van den Berg, M.P., de Kloet, E.R. and Vreugdenhil, E. (1999) MicroSAGE: a modified procedure for serial analysis of gene expression in limited amounts of tissue. Nucleic Acids Res., 27, 1300-1307.
27. Meier-Ewert, S., Lange, J., Gerst, H., Herwig, R., Schmitt, A., Freund, J., Elge, T., Mott, R., Herrmann, B. and Lehrach, H. (1998) Comparative gene expression profiling by oligonucleotide fingerprinting. Nucleic Acids Res., 26, 2216-2223.
28. Lipshutz, R.J., Morris, D., Chee, M., Hubbell, E., Kozal, M.J., Shah, N., Shen, N., Yang, R. and Fodor, S.P. (1995) Using oligonucleotide probe arrays to access genetic diversity. Biotechniques, 19, 442-447.
29. Chee, M., Yang, R., Hubbell, E., Berno, A., Huang, X.C., Stern, D., Winkler, J., Lockhart, D.J., Morris, M.S. and Fodor, S.P. (1996) Accessing genetic information with high-density DNA arrays. Science, 274, 610-614.
30. Lockhart, D.J., Dong, H., Byrne, M.C., Follettie, M.T., Gallo, M.V., Chee, M.S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H. and Brown, E.L. (1996) Expression monitoring by hybridization to high-density oligonucleotide arrays. Nature Biotechnol., 14, 1675-1680.
31. Wodicka, L., Dong, H., Mittmann, M., Ho, M.H. and Lockhart, D.J. (1997) Genome-wide expression monitoring in Saccharomyces cerevisiae. Nature Biotechnol., 15, 1359-1367.
32. Schena, M., Shalon, D., Heller, R., Chai, A., Brown, P. and Davis, R. (1996) Parallel human genome analysis: microarray-based expression monitoring of 1000 genes. Proc. Natl Acad. Sci. USA, 93, 10614-10619.
33. Lashkari, D.A., DeRisi, J.L., McCusker, J.H., Namath, A.F., Gentile, C., Hwang, S.Y., Brown, P.O. and Davis, R.W. (1997) Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc. Natl Acad. Sci. USA, 94, 13057-13062.
34. Schena, M. (1996) Genome analysis with gene expression microarrays. BioEssays, 18, 427-431.
35. Shalon, D., Smith, S.J. and Brown, P.O. (1996) A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res., 6, 639-645.
36. Schena, M., Shalon, D., Davis, R.W. and Brown, P.O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 270, 467-470.
37. Watson, A., Mazumder, A., Stewart, M. and Balasubramanian, S. (1998) Technology for microarray analysis of gene expression. Curr. Opin. Biotechnol., 9, 609-614.
38. Duggan, D.J., Bittner, M., Chen, Y., Meltzer, P. and Trent, J.M. (1999) Expression profiling using cDNA microarrays. Nature Genet., 21 (suppl. 1), 10-14.
39. Cheung, V.G., Morley, M., Aguilar, F., Massimi, A., Kucherlapati, R. and Childs, G. (1999) Making and reading microarrays. Nature Genet., 21 (suppl. 1), 15-19.
40. Brown, P.O. and Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays. Nature Genet., 21 (suppl. 1), 33-37.
41. Debouck, C. and Goodfellow, P.N. (1999) DNA microarrays in drug discovery and development. Nature Genet., 21 (suppl. 1), 48-50.
42. Schena, M., Heller, R.A., Theriault, T.P., Konrad, K., Lachenmeier, E. and Davis, R.W. (1998) Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol., 16, 301-306.
43. Strausberg, R.L., Dahl, C.A. and Klausner, R.D. (1997) New opportunities for uncovering the molecular basis of cancer. Nature Genet., 16 (suppl.), 415-516.
44. Hwang, D.M., Dempsey, A.A., Wang, R.X., Rezvani, M., Barrans, J.D., Dai, K.S., Wang, H.Y., Ma, H., Cukerman, E., Liu, Y.Q., Gu, J.R., Zhang, J.H., Tsui, S.K., Waye, M.M., Fung, K.P., Lee, C.Y. and Liew, C.C. (1997) A genome-based resource for molecular cardiovascular medicine: toward a compendium of cardiovascular genes. Circulation, 96, 4146-4203.
45. Ji, H., Liu, Y.E., Jia, T., Wang, M., Liu, J., Xiao, G., Joseph, B.K., Rosen, C. and Shi, Y.E. (1997) Identification of a breast cancer-specific gene, BCSG1, by direct differential cDNA sequencing. Cancer Res., 57, 759-764.
46. Adjaye, J., Daniels, R., Bolton, V. and Monk, M. (1997) cDNA libraries from single human preimplantation embryos. Genomics, 46, 337-344.
47. Shimizu-Matsumoto, A., Adachi, W., Mizuno, K., Inazawa, J., Nishida, K., Kinoshita, S., Matsubara, K. and Okubo, K. (1997) An expression profile of genes in human retina and isolation of a complementary DNA for a novel rod photoreceptor protein. Invest. Ophthalmol. Vis. Sci., 38, 2576-2585.
48. Mao, M., Fu, G., Wu, J.S., Zhang, Q.H., Zhou, J., Kan, L.X., Huang, Q.H., He, K.L., Gu, B.W., Han, Z.G., Shen, Y., Gu, J., Yu, Y.P., Xu, S.H., Wang, Y.X., Chen, S.J. and Chen, Z. (1998) Identification of genes expressed in human CD34 (+) hematopoietic stem/progenitor cells by expressed sequence tags and efficient full-length cDNA cloning. Proc. Natl Acad. Sci. USA, 95, 8175-8180.
49. Gubbay, J., Doyle, J.P., Skinner, M. and Heintz, N. (1998) Changing patterns of gene expression identify multiple steps during regression of rat prostate in vivo. Endocrinology, 139, 2935-2943.
50. Vasmatzis, G., Essand, M., Brinkmann, U., Lee, B. and Pastan, I. (1998) Discovery of three genes specifically expressed in human prostate by expressed sequence tag database analysis. Proc. Natl Acad. Sci. USA, 95, 300-304.
51. Nelson, P.S., Ng, W.L., Schummer, M., Tru, L.D., Liu, A.Y., Bumgarner, R.E., Ferguson, C., Dimak, A. and Hood, L. (1998) An expressed-sequence-tag database of the human prostate: sequence analysis of 1168 cDNA clones. Genomics, 47, 12-25.
52. Tanabe, K., Nakagomi, S., Kiryu-Seo, S., Namikawa, K., Imai, Y., Ochi, T., Tohyama, M. and Kiyama, H. (1999) Expressed-sequence-tag approach to identify differentially expressed genes following peripheral nerve axotomy. Brain Res. Mol. Brain Res., 64, 34-40.
53. Skvorak, A.B., Weng, Z., Yee, A.J., Robertson, N.G. and Morton, C.C. (1999) Human cochlear expressed sequence tags provide insight into cochlear gene expression and identify candidate genes for deafness. Hum. Mol. Genet., 8, 439-452.
54. Zhang, L., Zhou, W., Velculescu, V., Kern, S., Hruban, R., Hamilton, S., Vogelstein, B. and Kinzler, K. (1997) Gene expression profiles in normal and cancer cells. Science, 276, 1268-1272.
55. Madden, S.L., Galella, E.A., Zhu, J., Bertelsen, A.H. and Beaudry, G.A. (1997) SAGE transcript profiles for p53-dependent growth regulation. Oncogene, 15, 1079-1085.
56. Velculescu, V., Zhang, L., Zhou, W., Vogelstein, B., Basrai, M.D.B.Jr, Hieter, P., Vogelstein, B. and Kinzler, K. (1997) Characterization of the yeast transcriptome. Cell, 88, 243-251.
57. He, T.C., Sparks, A.B., Rago, C., Hermeking, H., Zawel, L., da Costa, L.T., Morin, P.J., Vogelstein, B. and Kinzler, K.W. (1998) Identification of c-MYC as a target of the APC pathway. Science, 281, 1509-1512.
58. Hibi, K., Liu, Q., Beaudry, G.A., Madden, S.L., Westra, W.H., Wehage, S.L., Yang, S.C., Heitmiller, R.F., Bertelsen, A.H., Sidransky, D. and Jen, J. (1998) Serial analysis of gene expression in non-small cell lung cancer. Cancer Res., 58, 5690-5694.
59. de Waard, V., van den Berg, B.M.M., Veken, J., Schultz-Heienbrok, R., Pannekoek, H. and van Zonneveld, A.J. (1999) Serial analysis of gene expression to assess the endothelial cell response to an atherogenic stimulus. Gene, 226, 1-8.
60. Anderson, N.L., Hofmann, J.P., Gemmell, A. and Taylor, J. (1984) Global approaches to quantitative analysis of gene-expression patterns observed by use of two-dimensional gel electrophoresis. Clin. Chem., 30, 2031-2036.
61. Audic, S. and Claverie, J.-M. (1997) The significance of digital gene expression profiles. Genome Res., 7, 986-995.
62. Burke, J., Wang, H., Hide, W. and Davison, D.B. (1998) Alternative gene form discovery and candidate gene selection from gene indexing projects. Genome Res., 8, 276-290.
63. Gautheret, D., Poirot, O., Lopez, F., Audic, S. and Claverie, J.-M. (1998) Alternate polyadenylation in human mRNAs: a large-scale analysis by EST clustering. Genome Res., 8, 524-530.
64. Wen, X., Fuhrman, S., Michaels, G.S., Carr, D.B., Smith, S., Barker, J.L. and Somogyi, R. (1998) Large-scale temporal gene expression mapping of central nervous system development. Proc. Natl Acad. Sci. USA, 95, 334-339.
65. Eisen, M.B., Spellman, P.T., Brown, P.O. and Botstein, D. (1998) Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
66. Michaels, G.S., Carr, D.B., Askenazi, M., Fuhrman, S., Wen, X. and Somogyi, R. (1998) Cluster analysis and data visualization of large-scale gene expression data. Pac. Symp. Biocomput., 42-53.
67. Greller, L.D. and Tobin, F.L. (1999) Detecting selective expression of genes and proteins. Genome Res., 9, 282-296.
68. Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Dmitrovsky, E., Lander, E.S. and Golub, T.R. (1999) Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc. Natl Acad. Sci. USA, 96, 2907-2912.
69. Vingron, M. and Hoheisel, J. (1999) Computational aspects of expression data. J. Mol. Med., 77, 3-7.
70. Ringwald, M., Davis, G.L., Smith, A.G., Trepanier, L.E., Begley, D.A., Richardson, J.E. and Eppig, J.T. (1997) The mouse gene expression database GXD. Semin. Cell Dev. Biol., 8, 489-497.
71. Davidson, D., Bard, J., Brune, R., Burger, A., Dubreuil, C., Hill, W., Kaufman, M., Quinn, J., Stark, M. and Baldock, R. (1997) The mouse atlas and graphical gene-expression database. Semin. Cell Dev. Biol., 8, 509-517.
72. Miller, G., Fuchs, R. and Lai, E. (1997) IMAGE cDNA clones, UniGene clustering and ACeDB: an integrated resource for expressed sequence information. Genome Res., 7, 1027-1032.
73. Bailey, L.C.Jr, Searls, D.B. and Overton, G.C. (1998) Analysis of EST-driven gene annotation in human genomic sequence. Genome Res., 8, 362-376.
74. Ermolaeva, O., Rastogi, M., Pruitt, K.D., Schuler, G.D., Bittner, M.L., Chen, Y., Simon, R., Meltzer, P., Trent, J.M. and Boguski, M.S. (1998) Data management and analysis for gene expression arrays. Nature Genet., 20, 19-23.
75. Bassett, D.E.Jr, Eisen, M.B. and Boguski, M.S. (1999) Gene expression informatics - it's all in your mine. Nature Genet., 21 (Suppl. 1), 51-55.
76. Stoeckert, C.J.Jr. Salas, F., Brunk, B. and Overton, G.C. (1999) EpoDB: a prototype database for the analysis of genes expressed during vertebrate erythropoiesis. Nucleic Acids Res., 27, 200-203.
77. Hawkins, V., Doll, D., Bumgarner, R., Smith, T., Abajian, C., Hood, L. and Nelson, P.S. (1999) PEDB: the Prostate Expression Database. Nucleic Acids Res., 27, 204-208.
78. Siegel, S. (1956) Nonparametric Methods for the Behavioral Sciences, McGraw-Hill, New York, NY.
79. Livak, K.J., Flood, S.J., Marmaro, J., Giusti, W. and Deetz, K. (1995) Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. PCR Methods Appl., 4, 357-362.
80. Somogyi, R., Wen, X., Ma, W. and Barker, J.L. (1995) Developmental kinetics of GAD family mRNAs parallel neurogenesis in the rat spinal cord. J. Neurosci., 15, 2575-2591.
81. 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) Gene expression profiling of alveolar Rhaddomyosarcoma with cDNA microarrays. Cancer Res., 58, 5009-5013.
82. DeRisi, J.L., Iyer, V.R. and Brown, P.O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278, 680-686.
83. Cho, R., Campbell, M., Winzeler, E., Steinmetz, L., Conway, A., Wodika, L., Wolfsberg, T., Gabrielian, A., Landsman, D., Lockhart, D. and Davis, R. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell, 2, 65-73.
84. 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) Comprehensive identification of cell cycle-regulated genes of the yeast S. cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
85. Chu, S., DeRisi, J., Eisen, M., Mulholland, J., Botstein, D., Brown, P.O. and Herskowitz, I. (1998) The transcriptional program of sporulation in budding yeast. Science, 282, 699-705.
86. 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., Boguski, M.S., Lashkari, D., Shalon, D., Botstein, D. and Brown, P.O. (1999) The transcriptional program in the response of human fibroblast to serum. Science, 283, 83-87.
87. D'Haeseleer, P., Wen, X., Fuhrman, S. and Somogyi, R. (1998) Mining the gene expression matrix: inferring gene relationships from large scale gene expression data (HTML). In Paton, R.C. and Holcombe, M. (eds), Information Processing in Cells and Tissues. Plenum Publishing, New York, NY, pp. 203-212.
88. Ewing, R.M., Ben Kahla, A., Poirot, O., Lopez, F., Audic, S. and Claverie, J.-M. (1999) Large-scale, statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res., 9, in press.
89. Fitch, W.M. and Margoliash, E. (1967) Construction of phylogenic trees. Science, 155, 279-284.
90. Felsenstein, J. (1993) PHYLIP (Phylogeny Inference Package) Version 3.5c. J. Felsenstein, Department of Genetics, University of Washington, Seattle, WA.
91. Felsenstein, J. (1989) PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics, 5, 164-166.
92. Can, D.B., Somogyi, R. and Michaels, G. (1997) Templates for looking at gene expression clustering. Stat. Comput. Stat. Graphics Newslett. (April), 20-29.
93. Matula, D.W. (1977) Graph theoretic techniques for cluster analysis algorithms. In van Ryzin, J. (ed.), Classification and Clustering. Academic Press, London, UK, pp. 95-129.
94. Ben-Dor, A. and Yakhini, Z. (1999) Clustering gene expression patterns. In Istrail, S., Pevzner, P. and Waterman, M. (eds), Recomb 99, ACM Press, Washington, DC, pp. 33-42.
95. Hartuv, E., Schmitt, A., Lange, J., Meirer-Ewert, S., Lehrach, H. and Shamir, R. (1999) An algorithm for clustering cDNAs for gene expression analysis. In Istrail, S., Pevzner, P. and Waterman, M. (eds), Recomb 99, ACM Press, Washington, DC, pp. 188-197.
96. Arkin, A., Shen, P. and Ross, J. (1997) A test case of correlation metric construction of a reaction pathway from measurements. Science, 277, 1275-1279.
97. Thieffry, D. and Thomas, R. (1998) Qualitative analysis of gene network. Pac. Symp. Biocomput., 77-87.
98. Michaels, G.S., Carr, D.B., Askenazi, M., Fuhrman, S., Wen, X. and Somogyi, R. (1998) Cluster analysis and data visualization of large-scale gene expression data. Pac. Symp. Biocomput., 42-53.
99. Somogyi, R. and Sniegoski, C.A. (1996) Modeling the complexity of genetic networks: understanding multigenic and pleiotropic regulation. Complexity, 1, 45-63.
100. Chen, T., Filkov, V. and Skiena, S.S. (1999) Identifying gene regulatory networks from experimental data. In Istrail, S., Pevzner, P. and Waterman, M. (eds), Recomb 99. ACM Press, Washington, DC, pp. 94-103.
101. Karp, R.M., Stoughton, R. and Yeung, K.Y. (1999) Algorithms for choosing differential gene expression experiments. In Istrail, S., Pevzner, P. and Waterman, M. (eds), Recomb 99. ACM Press, Washington, DC, pp. 208-217.
102. Chien, C.T., Bartel, P.L., Sternglanz, R. and Fields, S. (1991) The two-hybrid system: a method to identify and clone genes for proteins that interact with a protein of interest. Proc. Natl Acad. Sci. USA, 88, 9578-9582.
103. Brazma, A., Jonassen, I., Vilo, J. and Ukkonen, E. (1998) Predicting gene regulatory elements in silico on a genomic scale. Genome Res., 8, 1202-1215.
104. Myers, T.G., Anderson, N.L., Waltham, M., Li, G., Buolamwini, J.K., Scudiero, D.A., Paull, K.D., Sausville, E.A. and Weinstein, J.N. (1997) A protein expression database for the molecular pharmacology of cancer. Electrophoresis, 18, 647-653.
105. Anderson, L. and Seilhamer, J. (1997) A comparison of selected mRNA and protein abundances in human liver. Electrophoresis, 18, 533-537.
106. Weinstein, J.N., Myers, T.G., O'Connor, P.M., Friend, S.H., Fornace, A.J.Jr, Kohn, K.W., Fojo, T., Bates, S.E., Rubinstein, L.V., Anderson, N.L., Buolamwini, J.K., van Osdol, W.W., Monks, A.P., Scudiero, D.A., Sausville, E.A., Zaharevitz, D.W., Bunow, B., Viswanadhan, V.N., Johnson, G.S., Wittes, R.E. and Paull, K.D. (1997) An information-intensive approach to the molecular pharmacology of cancer. Science, 275, 343-349.
107. O'Connor, P.M., Jackman, J., Bae, I., Myers, T.G., Fan, S., Mutoh, M., Scudiero, D.A., Monks, A., Sausville, E.A., Weinstein, J.N., Friend, S., Fornace, A.J.Jr and Kohn, K.W. (1997) Characterization of the p53 tumor suppressor pathway in cell lines of the National Cancer Institute anticancer drug screen and correlations with the growth-inhibitory potency of 123 anticancer agents. Cancer Res., 57, 4285-4300.
108. Wosikowski, K., Schuurhuis, D., Johnson, K., Paull, K.D., Myers, T.G., Weinstein, J.N. and Bates, S.E. (1997) Identification of epidermal growth factor receptor and c-erbB2 pathway inhibitors by correlation with gene expression patterns. J. Natl Cancer Inst., 89, 1505-1515.
109. Liang, S., Fuhrman, S. and Somogyi, R. (1998) Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac. Symp. Biocomput., 18-29.