Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription

Nucleic Acids Research

Volumn 31, Issue 13, 2003, Pages 3824-3828

  Lapidot, Michal ^a   Pilpel, Yitzhak ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

ALGORITHM; ARTICLE; COMPUTER ANALYSIS; COMPUTER INTERFACE; CONTROLLED STUDY; EXPERIMENTAL DESIGN; GENE EXPRESSION PROFILING; INTERNET; MOLECULAR BIOLOGY; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; PROTEIN MOTIF; QUANTITATIVE ANALYSIS; REGULATORY SEQUENCE; RNA ANALYSIS; RNA TRANSCRIPTION; SENSITIVITY AND SPECIFICITY; STATISTICAL ANALYSIS; BIOSYNTHESIS; COMPUTER PROGRAM; DNA RESPONSIVE ELEMENT; DNA SEQUENCE; GENETIC TRANSCRIPTION; METHODOLOGY;

INTERNET; PROMOTER REGIONS (GENETICS); REGULATORY SEQUENCES, NUCLEIC ACID; RESPONSE ELEMENTS; RNA, MESSENGER; SEQUENCE ANALYSIS, DNA; SOFTWARE; TRANSCRIPTION, GENETIC;

EID: 0042120980     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg593     Document Type: Article

References (29)

1. Werner,T. (2002) Finding and decrypting of promoters contributes to the elucidation of gene function. In Silico Biol., 2, 249-255.
2. Tavazoie,S., Hughes,J.D., Campbell,M.J., Cho,R.J. and Church,G.M. (1999) Systematic determination of genetic network architecture. Nature Genet., 22, 281-285.
3. 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.
4. Wolfsberg,T.G., Gabrielian,A.E., Campbell,M.J., Cho,R.J., Spouge,J.L. and Landsman,D. (1999) Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae. Genome Res., 9, 775-792.
5. McCue,L.A., Thompson,W., Carmack,C.S. and Lawrence,C.E. (2002) Factors influencing the identification of transcription factor binding sites by cross-species comparison. Genome Res., 12, 1523-1532.
6. McGuire,A.M., Hughes,J.D. and Church,G.M. (2000) Conservation of DNA regulatory motifs and discovery of new motifs in microbial genomes. Genome Res., 10, 744-757.
7. Wasserman,W.W., Palumbo,M., Thompson,W., Fickett,J.W. and Lawrence,C.E. (2000) Human-mouse genome comparisons to locate regulatory sites. Nature Genet., 26, 225-228.
8. Mannhaupt,G., Schnall,R., Karpov,V., Vetter,I. and Feldmann,H. (1999) Rpn4p acts as a transcription factor by binding to PACE, a nonamer box found upstream of 26S proteasomal and other genes in yeast. FEBS Lett., 450, 27-34.
9. Su,A.I., Cooke,M.P., Ching,K.A., Hakak,Y., Walker,J.R., Wiltshire,T., Orth,A.P., Vega,R.G., Sapinoso,L.M., Moqrich,A. et al. (2002) Large-scale analysis of the human and mouse transcriptomes. Proc. Natl Acad. Sci. USA, 99, 4465-4470.
10. Harmer,S.L., Hogenesch,J.B., Straume,M., Chang,H.S., Han,B., Zhu,T., Wang,X., Kreps,J.A. and Kay,S.A. (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science, 290, 2110-2113.
11. Pilpel,Y., Sudarsanam,P. and Church,G.M. (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nature Genet., 29, 153-159.
12. Sudarsanam,P., Pilpel,Y. and Church,G.M. (2002) Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Saccharomyces cerevisiae. Genome Res., 12, 1723-1731.
13. Lenhard,B. and Wasserman,W.W. (2002) TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics, 18, 1135-1136.
14. Dudley,A.M., Rougeulle,C. and Winston,F. (1999) The Spt components of SAGA facilitate TBP binding to a promoter at a post-activator-binding step in vivo. Genes Dev., 13, 2940-2945.
15. Benos,P.V., Lapedes,A.S. and Stormo,G.D. (2002) Is there a code for protein-DNA recognition? Probab(ilistical)ly. Bioessays, 24, 466-475.
16. Benos,P.V., Bulyk,M.L. and Stormo,G.D. (2002) Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res., 30, 4442-4451.
17. Bulyk,M.L., Huang,X., Choo,Y. and Church,G.M. (2001) Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl Acad. Sci. USA, 98, 7158-7163.
18. Shen-Orr,S.S., Milo,R., Mangan,S. and Alon,U. (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genet., 31, 64-68.
19. 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.
20. 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.
21. Roberts,C.J., Nelson,B., Marton,M.J., Stoughton,R., Meyer,M.R., Bennett,H.A., He,Y.D., Dai,H., Walker,W.L., Hughes,T.R. et al. (2000) Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science, 287, 873-880.
22. Wagner,A. (1999) Genes regulated cooperatively by one or more transcription factors and their identification ih whole eukaryotic genomes. Bioinformatics, 15, 776-784.
23. Wagner,A. (1997) A computational genomics approach to the identification of gene networks. Nucleic Acids Res., 25, 3594-3604.
24. Frith,M.C., Hansen,U. and Weng,Z. (2001) Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics, 17, 878-889.
25. Hughes,J.D., Estep,P.W., Tavazoie,S. and Church,G.M. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205-1214.
26. Cho,R.J., Campbell,M.J., Winzeler,E.A., Steinmetz,L., Conway,A., Wodicka,L., Wolfsberg,T.G., Gabrielian,A.E., Landsman,D., Lockhart,D.J. et al. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell, 2, 65-73.
27. 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.
28. 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.
29. Jelinsky,S.A., Estep,P., Church,G.M. and Samson,L.D. (2000) Regulatory networks revealed by transcriptional profiling of damaged saccharomyces cerevisiae cells: rpn4 links base excision repair with proteasomes. Mol. Cell. Biol., 20, 8157-8167.