Prediction of regulatory networks: Genome-wide identification of transcription factor targets from gene expression data

Bioinformatics

Volumn 19, Issue 15, 2003, Pages 1917-1926

  Qian, Jiang ^a   Lin, Jimmy ^a   Luscombe, Nicholas M ^b   Yu, Haiyuan ^b   Gerstein, Mark ^b  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; CHROMOSOME STRUCTURE; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA ANALYSIS; DNA MICROARRAY; DNA VECTOR; GENE CLUSTER; GENE CONTROL; GENE EXPRESSION PROFILING; GENE TARGETING; GENETIC ANALYSIS; NONHUMAN; PREDICTION; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; VALIDATION PROCESS;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0142179209     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg347     Document Type: Article

References (34)

1. Alberts,B., Bray,D., Lewis,J., Raff,M., Roberts,K. and Watson,J. (1994) Molecular Biology of the Cell. Garland Publishing, New York.
2. An,A., Cercone,N. and Huang,X. (2001) A case study for learning from imbalanced data sets. Advances in Artificial Intelligence: Proceedings of the 14th Conference of the Canadian Society for Computational Studies of Intelligence, 1, 1-15.
3. Brown,M.P., Grundy,W.N., Lin,D., Cristianini,N., Sugnet,C.W., Furey,T.S., Ares,M.,Jr. and Haussler,D. (2000) Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc. Natl Acad. Sci. USA, 97, 262-267.
4. Burges,C.J.C. (1998) A tutorial on support vector machines for pattern recognition. Data Mining and Knowledge Discovery, 2, 121-167.
5. Devaux,F., Marc,P. and Jacq,C. (2001) Transcriptomes, transcription activators and microarrays. FEBS Lett., 498, 140-144.
6. 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.
7. Gasch,A.P., Spellman,P.T., Kao,C.M., Carmel-Harel,O., Eisen,M.B., Storz,G., Botstein,D. and Brown,P.O. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell., 11, 4241-4257.
8. Gerstein,M. and Jansen,R. (2000) The current excitement in bioinformatics-analysis of whole-genome expression data: how does it relate to protein structure and function? Curr. Opin. Struct. Biol., 10, 574-584.
9. Grabe,N. (2002) AliBaba2: context specific identification of transcription factor binding sites. In Silico Biol., 2, S1-S15.
10. Halfon,M.S., Grad,Y., Church,G.M. and Michelson,A.M. (2002) Computation-based discovery of related transcriptional regulatory modules and motifs using an experimentally validated combinatorial model. Genome Res., 12, 1019-1028.
11. Horak,C.E., Luscombe,N.M., Qian,J., Piccirrillo,S., Gerstein,M. and Snyder,M. (2002) Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev., 16, 3017-3033.
12. Iyer,V.R., Horak,C.E., Scafe,C.S., Botstein,D., Snyder,M. and Brown,P.O. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature, 409, 533-538.
13. Japkowicz,N. (2000) The class imbalance problem: significance and strategies. Proceedings of the 2000 International Conference on Artificial Intelligence, 1.
14. Japkowicz,N. and Stephen,S. (2002) The class imbalance problem: a systematic study. Intelligent Data Analysis, 6, 429-450.
15. Joachims,T. (1998) Text categorization with support vector machines: learning with many relevant features. In Proceedings of the European Conference on Machine Learning. Springer, Berlin.
16. Kel,A.E., Kel-Margoulis,O.V., Farnham,P.J., Bartley,S.M., Wingender,E. and Zhang,M.Q. (2001) Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors. J. Mol. Biol., 309, 99-120.
17. Krivan,W. and Wasserman,W.W. (2001) A predictive model for regulatory sequences directing liver-specific transcription. Genome Res., 11, 1559-1566.
18. Lee,T.I., Rinaldi,N.J., Robert,F., Odom,D.T., Bar-Joseph,Z., Gerber,G.K., Hannett,N.M., Harbison,C.T., Thompson,C.M., Simon,I. et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298, 799-804.
19. Ly,D.H., Lockhart,D.J., Lerner,R.A. and Schultz,P.G. (2000) Mitotic misregulation and human aging. Science, 287, 2486-2492.
20. Qian,J., Dolled-Filhart,M., Lin,J., Yu,H. and Gerstein,M. (2001) Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions. J. Mol. Biol., 314, 1053-1066.
21. Ren,B., Robert,F., Wyrick,J.J., Aparicio,O., Jennings,E.G., Simon,I., Zeitlinger,J., Schreiber,J., Hannett,N., Kanin,E. et al. (2000) Genome-wide location and function of DNA binding proteins. Science, 290, 2306-2309.
22. Riechmann,J.L., Heard,J., Martin,G., Reuber,L., Jiang,C., Keddie,J., Adam,L., Pineda,O., Ratcliffe,O.J., Samaha,R.R. et al. (2000a) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 290, 2105-2110.
23. Riechmann,J.L., Heard,J., Martin,G., Reuber,L., Jiang,C., Keddie,J., Adam,L., Pineda,O., Ratcliffe,O.J., Samaha,R.R. et al. (2000b) Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. Science, 290, 2105-2110.
24. Roulet,E., Fisch,I., Junier,T., Bucher,P. and Mermod,N. (1998) Evaluation of computer tools for the prediction of transcription factor binding sites on genomic DNA. In Silico Biol., 1, 21-28.
25. Schuldiner,O., Yanover,C. and Benvenisty,N. (1998) Computer analysis of the entire budding yeast genome for putative targets of the GCN4 transcription factor. Curr. Genet., 33, 16-20.
26. Snyder,M. and Gerstein,M. (2003) Genomics. Defining genes in the genomics era. Science, 300, 258-260.
27. 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 Saccharomyces Cerevisiae by microarray hybridization. Mol. Biol. Cell., 9, 3273-3297.
28. Tan,K., Moreno-Hagelsieb,G., Collado-Vides,J. and Stormo,G.D. (2001) A comparative genomics approach to prediction of new members of regulons. Genome Res., 11, 566-584.
29. Tupler,R., Perini,G., Pellegrino,M.A. and Green,M.R. (1999) Profound misregulation of muscle-specific gene expression in facioscapulohumeral muscular dystrophy. Proc. Natl Acad. Sci. USA, 96, 12650-12654.
30. Vapnik,V. (1998) Statistical Learning Theory. Wiley, New York.
31. Vladimir,N. and Vapnik,V. (1995) The Nature of Statistical Learning Theory. Springer, Berlin.
32. Wingender,E., Chen,X., Fricke,E., Geffers,R., Hehl,R., Liebich,I., Krull,M., Matys,V., Michael,H., Ohnhauser,R. et al. (2001) The TRANSFAC system on gene expression regulation. Nucleic Acids Res., 29, 281-283.
33. Zhu,J. and Zhang,M.Q. (1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15, 607-611.
34. Zhu,Z., Pilpel,Y. and Church,G.M. (2002) Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm. J. Mol. Biol., 318, 71-81.