Identification of transcription factor targets by phenotypic activation and microarray expression profiling in yeast

Methods in Molecular Biology

Volumn 548, Issue , 2009, Pages 19-35

  Chua, Gordon ^a  

^a UNIVERSITY OF CALGARY   (Canada)

Author keywords

FunSpec; Microarray; Overexpression; Phenotypic activation; RankMotif; Transcription factor; Yeast

Indexed keywords

COMPLEMENTARY DNA; FUNGAL DNA; FUNGAL RNA; MESSENGER RNA; SACCHAROMYCES CEREVISIAE PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; DNA MICROARRAY; FUNGAL GENE; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PHENOTYPE; PROMOTER REGION; SACCHAROMYCES CEREVISIAE; STATISTICS;

BASE SEQUENCE; BINDING SITES; DNA, COMPLEMENTARY; DNA, FUNGAL; GENE EXPRESSION PROFILING; GENES, FUNGAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OPEN READING FRAMES; PHENOTYPE; PROMOTER REGIONS, GENETIC; RNA, FUNGAL; RNA, MESSENGER; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS;

EID: 67849095319     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-540-4_2     Document Type: Article

References (13)

1. Chua, G., Robinson, M. D., Morris, Q., and Hughes, T. R. (2004). Transcriptional networks: reverse-engineering gene regulation on a global scale. Curr. Opin. Microbiol. 7, 638-646. (Pubitemid 39536291)
2. Sopko, R., Huang, D., Preston, N., Chua, G., Papp, B., Kafadar, K., Snyder, M., Oliver, S. G., Cyert, M., Hughes, T. R., Boone, C., and Andrews, B. (2006). Mapping pathways and phenotypes by systematic gene overexpression. Mol. Cell 21, 319-330. (Pubitemid 43163527)
3. Chua, G., Morris, Q. D., Sopko, R., Robinson, M. D., Ryan, O., Chan, E. T., Frey, B. J., Andrews, B. J., Boone, C., and Hughes T. R. (2006). Identifying transcription factor functions and targets by phenotypic activation. Proc. Natl. Acad. Sci. USA 103, 12045-12050. (Pubitemid 44215808)
4. Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton, R., Armour, C. D., Bennett, H. A., Coffey, E., Dai, H., He, Y. D., Kidd, M. J., King, A. M., Meyer, M. R., Slade, D., Lum, P. Y., Stepaniants, S. B., Shoemaker, D. D., Gachotte, D., Chakraburtty, K., Simon, J., Bard, M., and Friend, S. H. (2000). Functional discovery via a compendium of expression profiles. Cell 102, 109-126.
5. Grigull, J., Mnaimneh, S., Pootoolal, J., Robinson, M. D., and Hughes, T. R. (2004). Genome-wide analysis of mRNA stability using transcription inhibitors and microarrays reveals posttranscriptional control of ribosome biogenesis factors. Mol. Cell. Biol. 24, 5534-5547. (Pubitemid 38738184)
6. Robinson, M. D., Griqull, J., Mohammad, N., and Hughes, T. R. (2002). FunSpec: a web-based cluster interpreter for yeast. BMC Bioinformatics 3, 35.
7. Mnaimneh, S., Davierwala, A. P., Haynes, J., Moffat, J., Peng, W.-T., Zhang, W., Yang, X., Pootoolal, J., Chua, G., Lopez, A., Trochesset, M., Morse, D., Krogan, N. J., Hiley, S. L., Li, Z., Morris, Q., Grigull, J., Mitsakakis, N., Roberts, C. J., Greenblatt, J. F., Boone, C., Kaiser, C. A., Andrews, B. J., and Hughes, T. R. (2004.) Exploration of essential gene functions via titratable promoter alleles. Cell 118, 31-44. (Pubitemid 38902812)
8. Gelperin, D. M., White, M. A., Wilkinson, M. L., Kon, Y., Kung, L. A., Wise, K. J., Lopez-Hoyo, N., Jiang, L., Piccirillo, S., Yu, H., Gerstein, M., Dumont, M. E., Phizicky, E. M., Synder, M., and Grayhach, E. J. (2005). Biochemical and genetic analysis of the yeast proteome with a movable ORF collection. Genes Dev. 19, 2816-2826. (Pubitemid 41739967)
9. Luscombe, N. M., Austin, S. E., Berman, H. M., and Thornton, J. M. (2000). An overview of the structures of protein-DNA complexes. Genome Biol. 1, REVIEWS001.
10. 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., Tyers, M., Boone, C., and Friend, S. H. (2000). Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287, 873-880. (Pubitemid 30084333)
11. Berger, M. F., Philippakis, A. A., Qureshi, A. M., He, F. S., Estep, P. W. III, and Bulyk, M. L. (2006). Compact, universal DNA microarrays to comprehensively determine transcription factor binding site specificities. Nat. Biotechnol. 24, 1429-1435. (Pubitemid 44722107)
12. Chen, X., Hughes, T. R., and Morris, Q. (2007). RankMotif ++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors. Bioinformatics 23, i72-i79. (Pubitemid 47244388)
13. Liu, X., Brutlag, D. L., and Liu, J. S. (2001). BioProspector: discovering conserved DNA motifs in upstream regulatory regions of coexpressed genes. Pac. Symp. Biocomput. 6, 127-138.