Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal?

Trends in Genetics

Volumn 24, Issue 7, 2008, Pages 319-323

  Balaji, S ^a   Iyer, Lakshminarayan M ^a   Babu, M Madan ^b   Aravind, L ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

BIOGENESIS; CHROMATIN IMMUNOPRECIPITATION; GENOME; PRIORITY JOURNAL; PROTEIN AGGREGATION; PROTEIN EXPRESSION; PROTEIN FOLDING; RIBOSOME; SHORT SURVEY; TELOMERE; TRANSCRIPTION REGULATION;

GENE EXPRESSION REGULATION; GENE REGULATORY NETWORKS; GENETIC TECHNIQUES; PROTEIN BIOSYNTHESIS; TELOMERE; TRANSCRIPTION, GENETIC;

EID: 45449093756     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2008.04.006     Document Type: Short Survey

References (18)

1. Svetlov V.V., and Cooper T.G. Review: compilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae. Yeast 11 (1995) 1439-1484
2. Guelzim N., et al. Topological and causal structure of the yeast transcriptional regulatory network. Nat. Genet. 31 (2002) 60-63
3. Harbison C.T., et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431 (2004) 99-104
4. Lee T.I., et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298 (2002) 799-804
5. Horak C.E., et al. Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev. 16 (2002) 3017-3033
6. Hu Z., et al. Genetic reconstruction of a functional transcriptional regulatory network. Nat. Genet. 39 (2007) 683-687
7. Chua G., et al. Identifying transcription factor functions and targets by phenotypic activation. Proc. Natl. Acad. Sci. U. S. A. 103 (2006) 12045-12050
8. Hughes T.R., et al. Functional discovery via a compendium of expression profiles. Cell 102 (2000) 109-126
9. Balaji S., et al. Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks. J. Mol. Biol. 360 (2006) 204-212
10. Marion R.M., et al. Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression. Proc. Natl. Acad. Sci. U. S. A. 101 (2004) 14315-14322
11. Jorgensen P., et al. A dynamic transcriptional network communicates growth potential to ribosome synthesis and critical cell size. Genes Dev. 18 (2004) 2491-2505
12. Komili S., et al. Functional specificity among ribosomal proteins regulates gene expression. Cell 131 (2007) 557-571
13. Babu M.M., et al. Estimating the prevalence and regulatory potential of the telomere looping effect in yeast transcription regulation. Cell Cycle 5 (2006) 2354-2363
14. Wilson M.A., et al. The 1.1-A resolution crystal structure of DJ-1, the protein mutated in autosomal recessive early onset Parkinson's disease. Proc. Natl. Acad. Sci. U. S. A. 100 (2003) 9256-9261
15. Babu M.M., et al. Structure and evolution of transcriptional regulatory networks. Curr. Opin. Struct. Biol. 14 (2004) 283-291
16. Barabasi A.L., and Oltvai Z.N. Network biology: understanding the cell's functional organization. Nat. Rev. Genet. 5 (2004) 101-113
17. Schlitt T., and Brazma A. Modelling in molecular biology: describing transcription regulatory networks at different scales. Philos. Trans. R. Soc. Lond. B Biol. Sci. 361 (2006) 483-494
18. Huerta A.M., et al. RegulonDB: a database on transcriptional regulation in Escherichia coli. Nucleic Acids Res. 26 (1998) 55-59