Construction and application of a protein and genetic interaction network (yeast interactome)

Nucleic Acids Research

Volumn 37, Issue 7, 2009, Pages

  Stuart, Gregory R ^a   Copeland, William C ^a   Strand, Micheline K ^a,b  

^a NATIONAL INSTITUTE OF ENVIRONMENTAL HEALTH SCIENCES   (United States)

^b U S ARMY RESEARCH OFFICE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; TRANSCRIPTION FACTOR; GLYCEROL; SACCHAROMYCES CEREVISIAE PROTEIN;

ANALYTIC METHOD; ARTICLE; AUTOMATION; CELL METABOLISM; COMPUTER NETWORK; COMPUTER PROGRAM; DATA ANALYSIS; FUNGAL GENETICS; GENE CONTROL; GENE EXPRESSION; GENETIC DATABASE; INFORMATION PROCESSING; INTERNET; METABOLIC REGULATION; METABOLOME; MICROARRAY ANALYSIS; MOLECULAR INTERACTION; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; YEAST; DRUG EFFECT; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; METABOLISM;

SACCHAROMYCES;

GENE EXPRESSION REGULATION, FUNGAL; GENE REGULATORY NETWORKS; GLYCEROL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SOFTWARE; TRANSCRIPTION FACTORS;

EID: 64549099468     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp140     Document Type: Article

References (28)

1. Shannon,P., Markiel,A., Ozier,O., Baliga,N.S., Wang,J.T., Ramage,D., Amin,N., Schwikowski,B. and Ideker,T. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res., 13, 2498-2504.
2. Strand,M.K., Stuart,G.R., Longley,M.J., Graziewicz,M.A., Dominick,O.C. and Copeland,W.C. (2003) POS5 gene of Saccharomyces cerevisiae encodes a mitochondrial NADH kinase required for stability of mitochondrial DNA. Eukaryot. Cell, 2, 809-820.
3. Stuart,G.A., Humble,M.M., Strand,M.K. and Copeland,W.C. (2009) Transcriptional response to mitochondrial NADH kinase deficiency in Saccharomyces cerevisiae. Mitochondrion, In press
4. Spencer,F., Hugerat,Y., Simchen,G., Hurko,O., Connelly,C. and Hieter,P. (1994) Yeast kar1 mutants provide an effective method for YAC transfer to new hosts. Genomics, 22, 118-126.
5. Teixeira,M.C., Monteiro,P., Jain,P., Tenreiro,S., Fernandes,A.R., Mira,N.P., Alenquer,M., Freitas,A.T., Oliveira,A.L. and Sá-Correia,I. (2006) The YEASTRACT database: A tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res., 34, D446-D451.
6. Bonander,N., Ferndahl,C., Mostad,P., Wilks,M.D.B., Chang,C., Showe,L., Gustafsson,L., Larsson,C. and Bill,R.M. (2008) Transcriptome analysis of a respiratory Saccharomyces cerevisiae strain suggests the expression of its phenotype is glucose insensitive and predominantly controlled by Hap4, Cat8 and Mig1. BMC Genomics, 9, 365.
7. 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.
8. Maris,A.F., Assumpçào,A.L.K., Bonatto,D., Brendel,M. and Henriques,J.A.P. (2001) Diauxic shift-induced stress resistance against hydroperoxides in Saccharomyces cerevisiae is not an adaptive stress response and does not depend on functional mitochondria. Curr. Genet., 39, 137-149.
9. Kuhn,K.M., DeRisi,J.L., Brown,P.O. and Sarnow,P. (2001) Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol. Cell Biol., 21, 916-927.
10. Young,E.T., Dombek,K.M., Tachibana,C. and Ideker,T. (2003) Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8. J. Biol. Chem., 278, 26146-26158.
11. Ohlmeier,S., Kastaniotis,A.J., Hiltunen,J.K. and Bergmann,U. (2004) The yeast mitochondrial proteome, a study of fermentative and respiratory growth. J. Biol. Chem., 279, 3956-3979.
12. Xie,X., Wilkinson,H.H., Correa,A., Lewis,Z.A., Bell-Pedersen,D. and Ebbole,D.J. (2004) Transcriptional response to glucose starvation and functional analysis of a glucose transporter of Neurospora crassa. Fungal Genet. Biol., 41, 1104-1119.
13. Stuart,G.R., Santos,J.H., Strand,M.K., Van Houten,B. and Copeland,W.C. (2006) Mitochondrial and nuclear DNA defects in Saccharomyces cerevisiae with mutations in DNA polymerase γ associated with progressive external ophthalmoplegia. Hum. Mol. Genet., 15, 363-374.
14. Graziewicz,M.A., Longley,M.J. and Copeland,W.C. (2006) DNA polymerase γ in mitochondrial DNA replication and repair. Chem. Rev., 106 383-405.
15. Chan,S.S.L. and Copeland,W.C. (2008) DNA polymerase gamma and mitochondrial disease: Understanding the consequence of POLG mutations. Biochimica et Biophysica Acta. In press [29 October, 2008, Epub ahead of print]
16. Strand, M.K. and Copeland, W.C. (2002) Measuring mtDNA mutation rates in Saccharomyces cerevisiae using the mtArg8 assay, Methods Mol. Biol. 197, 151-157.
17. Lagunas,R. (1976) Energy metabolism of Saccharomyces cerevisiae discrepancy between ATP balance and known metabolic functions. Biochim. Biophys. Acta, 440, 661-674.
18. Rosenfeld,E. and Beauvoit,B. (2003) Role of the non-respiratory pathways in the utilization of molecular oxygen by Saccharomyces cerevisiae. Yeast, 20, 1115-1144.
19. Lin,S.-J., Kaeberlein,M., Andalis,A.A., Sturtz,L.A., Defossez,P.-A., Culotta,V.C., Fink,G.R. and Guarente,L. (2002) Calorie restriction extends Saccharomyces cerevisiae lifespan by increasing respiration. Nature, 418, 344-348.
20. Johnston,M. and Kim,J.-H. (2005) Glucose as a hormone: Receptor-mediated glucose sensing in the yeast Saccharomyces cerevisiae. Biochem. Soc. Trans., 33, 247-252.
21. Jackson,M.J., Papa,S., Bolaños,J., Bruckdorfer,R., Carlsen,H., Elliott,R.M., Flier,J., Griffiths,H.R., Heales,S., Holst,B. et al. (2002) Antioxidants, reactive oxygen and nitrogen species, gene induction and mitochondrial function. Mol. Aspects Med., 23, 209-285.
22. Grant,C.M., Perrone,G. and Dawes,I.W. (1998) Glutathione and catalase provide overlapping defenses for protection against hydrogen peroxide in the yeast Saccharomyces cerevisiae. Biochem. Biophys. Res. Commun. 253, 893-898.
23. Futcher,B. (2002) Transcriptional regulatory networks and the yeast cell cycle. Curr. Opin. Cell Biol., 14, 676-683.
24. 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.
25. Begley,T.J. and Samson,L.D. (2004) Network responses to DNA damaging agents. DNA Repair, 3, 1123-1132.
26. Tong,A.H.Y., Lesage,G., Bader,G.D., Ding,H., Xu,H., Xin,X., Young,J., Berriz,G.F., Brost,R.L., Chang,M. et al. (2004) Global mapping of the yeast genetic interaction network. Science, 303, 808-813.
27. Wu,W.-S., Li,W.-H. and Chen,B.-S. (2006) Computational reconstruction of transcriptional regulatory modules of the yeast cell cycle. BMC Bioinformatics, 7, 421.
28. Boone,C., Bussey,H. and Andrews,B.J. (2007) Exploring genetic interactions and networks with yeast. Nat. Rev. Genet, 8, 437-449.