Understanding gene sequence variation in the context of transcription regulation in yeast

PLoS Genetics

Volumn 6, Issue 1, 2010, Pages

  Gat Viks, Irit ^a   Meller, Renana ^b   Kupiec, Martin ^b   Shamir, Ron ^b  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

MEMBRANE PROTEIN; PROTEIN SWI; REGULATOR PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; CELL RESPIRATION; CONTROLLED STUDY; DNA POLYMORPHISM; FUNGAL STRAIN; GENE; GENE CONTROL; GENE EXPRESSION; GENE MAPPING; GENE SEGREGATION; GENE SEQUENCE; GENETIC LINKAGE; GENETIC VARIABILITY; GENOTYPE; MITOCHONDRION; MUTANT; NONHUMAN; QUANTITATIVE TRAIT LOCUS; SACCHAROMYCES CEREVISIAE; SPOROGENESIS; TRANSCRIPTION REGULATION; YEAST; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC TRANSCRIPTION; GENETICS; METABOLISM;

GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, FUNGAL; GENETIC VARIATION; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC;

EID: 76749169863     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1000800     Document Type: Article

References (30)

1. Brem RB, Yvert G, Clinton R, Kruglyak L (2002) Genetic dissection of transcriptional regulation in budding yeast. Science 296: 752-755.
2. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, et al. (2004) Genetic analysis of genome-wide variation in human gene expression. Nature 430: 743-747.
3. Schadt EE, Lamb J, Yang X, Zhu J, Edwards S, et al. (2005) An integrative genomics approach to infer causal associations between gene expression and disease. Nat Genet 37: 710-717.
4. Lee SI, Pe'er D, Dudley AM, Church GM, Koller D (2006) Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. Proc Natl Acad Sci U S A 103: 14062-14067.
5. Zhu J, Zhang B, Smith EN, Drees B, Brem RB, et al. (2008) Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks. Nat Genet 40: 854-861.
6. Yvert G, Brem RB, Whittle J, Akey JM, Foss E, et al. (2003) Trans-acting regulatory variation in Saccharomyces cerevisiae and the role of transcription factors. Nat Genet 35: 57-64.
7. Tu Z, Wang L, Arbeitman MN, Chen T, Sun F (2006) An integrative approach for causal gene identification and gene regulatory pathway inference. Bioinformatics 22: e489-496.
8. Kliebenstein DJ, West MA, van Leeuwen H, Loudet O, Doerge RW, et al. (2006) Identification of QTLs controlling gene expression networks defined a priori. BMC Bioinformatics 7: 308.
9. Suthram S, Beyer A, Karp RM, Eldar Y, Ideker T (2008) eQED: an efficient method for interpreting eQTL associations using protein networks. Mol Syst Biol 4: 162.
10. Sun W, Yu T, Li KC (2007) Detection of eQTL modules mediated by activity levels of transcription factors. Bioinformatics 23: 2290-2297.
11. Kulp DC, Jagalur M (2006) Causal inference of regulator-target pairs by gene mapping of expression phenotypes. BMC Genomics 7: 125.
12. Lee SI, Dudley AM, Drubin D, Silver PA, Krogan NJ, et al. (2009) Learning a prior on regulatory potential from eQTL data. PLoS Genet 5: e1000358.
13. Litvin O, Causton HC, Chen BJ, Pe'er D (2009) Special Feature: Modularity and interactions in the genetics of gene expression. Proc Natl Acad Sci U S A.
14. Ye C, Galbraith SJ, Liao JC, Eskin E (2009) Using network component analysis to dissect regulatory networks mediated by transcription factors in yeast. PLoS Comput Biol 5: e1000311.
15. Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, et al. (2000) Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles. Science 287: 873-880.
16. Hu Z, Killion PJ, Iyer VR (2007) Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet 39: 683-687.
17. Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y, et al. (2002) Revealing modular organization in the yeast transcriptional network. Nat Genet 31: 370-377.
18. Smith EN, Kruglyak L (2008) Gene-environment interaction in yeast gene expression. PLoS Biol 6: e83.
19. Gaisne M, Becam AM, Verdiere J, Herbert CJ (1999) A 'natural' mutation in Saccharomyces cerevisiae strains derived from S288c affects the complex regulatory gene HAP1 (CYP1). Curr Genet 36: 195-200.
20. Flynn PJ, Reece RJ (1999) Activation of transcription by metabolic intermediates of the pyrimidine biosynthetic pathway. Mol Cell Biol 19: 882-888.
21. Xie J, Pierce M, Gailus-Durner V, Wagner M, Winter E, et al. (1999) Sum1 and Hst1 repress middle sporulation-specific gene expression during mitosis in Saccharomyces cerevisiae. Embo J 18: 6448-6454.
22. McCord R, Pierce M, Xie J, Wonkatal S, Mickel C, et al. (2003) Rfm1, a novel tethering factor required to recruit the Hst1 histone deacetylase for repression of middle sporulation genes. Mol Cell Biol 23: 2009-2016.
23. Kellis M, Patterson N, Endrizzi M, Birren B, Lander ES (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423: 241-254.
24. Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, et al. (2003) Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301: 71-76.
25. Jiang F, Ryan MT, Schlame M, Zhao M, Gu Z, et al. (2000) Absence of cardiolipin in the crd1 null mutant results in decreased mitochondrial membrane potential and reduced mitochondrial function. J Biol Chem 275: 22387-22394.
26. Stranger BE, Forrest MS, Clark AG, Minichiello MJ, Deutsch S, et al. (2005) Genome-wide associations of gene expression variation in humans. PLoS Genet 1: e78.
27. Chesler EJ, Lu L, Shou S, Qu Y, Gu J, et al. (2005) Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat Genet 37: 233-242.
28. Geiss GK, Bumgarner RE, Birditt B, Dahl T, Dowidar N, et al. (2008) Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 26: 317-325.
29. Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, et al. (2005) EXPANDER-an integrative program suite for microarray data analysis. BMC Bioinformatics 6: 232.
30. Primig M, Williams RM, Winzeler EA, Tevzadze GG, Conway AR, et al. (2000) The core meiotic transcriptome in budding yeasts. Nat Genet 26: 415-423.