Global response of Saccharomyces cerevisiae to an alkylating agent
Open accessAbstract
DNA chip technology enables simultaneous examination of how ≈6,200 Saccharomyces cerevisiae gene transcript levels, representing the entire genome, respond to environmental change. By using chips bearing oligonucleotide arrays, we show that, after exposure to the alkylating agent methyl methanesulfonate, ≈325 gene transcript levels are increased and ≈76 are decreased. Of the 21 genes that already were known to be induced by a DNA-damaging agent, 18 can be scored as inducible in this data set, and surprisingly, most of the newly identified inducible genes are induced even more strongly than these 18. We examined 42 responsive and 8 nonresponsive ORFs by conventional Northern blotting, and 48 of these 50 ORFs responded as they did by DNA chip analysis, with magnitudes displaying a correlation coefficient of 0.79. Responsive genes fall into several expected and many unexpected categories. Evidence for the induction of a program to eliminate and replace alkylated proteins is presented.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Approximately 5% of the yeast genome is upregulated in response to various DNA-damaging agents.
“Indeed, approximately 5% of the yeast genome is upregulated in response to various DNA-damaging agents (15, 23, 24).”
From A Role for Checkpoint Kinase-Dependent Rad26 Phosphorylation in Transcription-Coupled DNA Repair in <i>Saccharomyces cerevisiae</i> (2010) · cites this paper as [24]
Cites
Molecular cloning: A laboratory manual
Deininger, P. L. (1990) · Analytical Biochemistry · doi:10.1016/0003-2697(90)90595-z · Cited by 84,684 · see citing works
Friedberg, E. C., Walker, G. C., Siede, W., Wood, R. D., Schultz, R. A., & Ellenberger, T. (2005) · doi:10.1128/9781555816704 · Cited by 5,683 · see citing works
Expression monitoring by hybridization to high-density oligonucleotide arrays
Lockhart, D. J., Dong, H., Byrne, M. C., Follettie, M. T., Gallo, M. V., Chee, M. S., Mittmann, M., Wang, C., Kobayashi, M., Norton, H., et al. (1996) · Nature Biotechnology · doi:10.1038/nbt1296-1675 · Cited by 2,841 · see citing works
Bootsma, D., & Hoeijmakers, J. H. J. (1996) · Trends in Genetics · doi:10.1016/0168-9525(96)81408-9 · Cited by 2,286 · see citing works
A Genome-Wide Transcriptional Analysis of the Mitotic Cell Cycle
Cho, R. J., Campbell, M. J., Winzeler, E. A., Steinmetz, L. M., Conway, A. R., Wodicka, L. M., Wolfsberg, T. G., Gabrielian, A. E., Landsman, D., Lockhart, D. J., et al. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80114-8 · Cited by 2,024 · see citing works
A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae
Schmitt, M. E., Brown, T. A., & Trumpower, B. L. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.10.3091 · Cited by 1,344 · see citing works
SGD: Saccharomyces Genome Database
Cherry, J. M. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.1.73 · Cited by 1,145 · see citing works
Genome-wide expression monitoring in Saccharomyces cerevisiae
Wodicka, L. M., Dong, H., Mittmann, M., Ho, M.-H., & Lockhart, D. J. (1997) · Nature Biotechnology · doi:10.1038/nbt1297-1359 · Cited by 973 · see citing works
Characterization of the Yeast Transcriptome
Velculescu, V. E., Zhang, L., Zhou, W., Vogelstein, R. J., Basrai, M. A., Bassett, D. E., Hieter, P., Vogelstein, B., & Kinzler, K. W. (1997) · Cell · doi:10.1016/s0092-8674(00)81845-0 · Cited by 973 · see citing works
DNA damage-inducible transcripts in mammalian cells.
Fornace, A. J., Alamo, I., & Hollander, M. C. (1988) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.85.23.8800 · Cited by 624 · see citing works
Shoemaker, D. D., Lashkari, D. A., Morris, D., Mittmann, M., & Davis, R. W. (1996) · Nature Genetics · doi:10.1038/ng1296-450 · Cited by 569 · see citing works
The H2O2 Stimulon in Saccharomyces cerevisiae
Godon, C., Lagniel, G., Lee, J., Buhler, J., Kieffer‐Jaquinod, S., Perrot, M., Boucherie, H., Tolédano, M. B., & Labarre, J. (1998) · Journal of Biological Chemistry · doi:10.1074/jbc.273.35.22480 · Cited by 566 · see citing works
Induction of Cellular p53 Activity by DNA-Damaging Agents and Growth Arrest
Zhan, Q., Carrier, F., & Fornace, A. J. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.7.4242 · Cited by 441 · see citing works
Cheng, J., Sheldon, E. L., Wu, L., Uribe, A., Gerrue, L. O., Carrino, J. J., Heller, M. J., & O'Connell, J. P. (1998) · Nature Biotechnology · doi:10.1038/nbt0698-541 · Cited by 348 · see citing works
Degradation of Oxidized Proteins in K562 Human Hematopoietic Cells by Proteasome
Grune, T., Reinheckel, T., & Davies, K. J. A. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.26.15504 · Cited by 328 · see citing works
Activity of Ubiquitin-dependent Pathway in Response to Oxidative Stress
Shang, F., Gong, X., & Taylor, A. (1997) · Journal of Biological Chemistry · doi:10.1074/jbc.272.37.23086 · Cited by 231 · see citing works
MIPS: a database for protein sequences, homology data and yeast genome information
Mewes, H., Albermann, K., Heumann, K., Liebl, S., & Pfeiffer, F. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.1.28 · Cited by 227 · see citing works
Landers, J. E., Cassel, S., & George, D. L. (1997) · PubMed · Cited by 210 · see citing works
Specific Saccharomyces cerevisiae genes are expressed in response to DNA-damaging agents.
Ruby, S. W., & Szostak, J. W. (1985) · Molecular and Cellular Biology · doi:10.1128/mcb.5.1.75 · Cited by 153 · see citing works
Chen, J., Derfler, B. H., & Samson, L. D. (1990) · The EMBO Journal · doi:10.1002/j.1460-2075.1990.tb07910.x · Cited by 144 · see citing works
Self-citationChen, J., Derfler, B. H., Maskati, A., & Samson, L. D. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.20.7961 · Cited by 125 · see citing works
Self-citationSpecific transcripts are elevated in Saccharomyces cerevisiae in response to DNA damage.
McClanahan, T., & Entee, K. M. (1984) · Molecular and Cellular Biology · doi:10.1128/mcb.4.11.2356 · Cited by 105 · see citing works
Kawaguchi, Y., Sant, C. V., & Roizman, B. (1998) · Journal of Virology · doi:10.1128/jvi.72.3.1731-1736.1998 · Cited by 84 · see citing works
Kiser, G. L., & Weinert, T. A. (1996) · Molecular Biology of the Cell · doi:10.1091/mbc.7.5.703 · Cited by 76 · see citing works
Herrlich, P. A., Blattner, C., Knebel, A., Bender, K. J., & Rahmsdorf, H. J. (1997) · Biological Chemistry · doi:10.1515/bchm.1997.378.11.1217 · Cited by 70 · see citing works
Preferential Translation of Reovirus mRNA by a σ3-Dependent Mechanism
Schmechel, S. C., Chute, M., Skinner, P. J., Anderson, R., & Schiff, L. A. (1997) · Virology · doi:10.1006/viro.1997.8531 · Cited by 67 · see citing works
Replication protein A binds to regulatory elements in yeast DNA repair and DNA metabolism genes.
Singh, K. K., & Samson, L. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.11.4907 · Cited by 60 · see citing works
Self-citationXiao, W., Singh, K. K., Chen, B., & Samson, L. D. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.12.7213 · Cited by 53 · see citing works
Self-citationChen, J., & Samson, L. D. (1991) · Nucleic Acids Research · doi:10.1093/nar/19.23.6427 · Cited by 45 · see citing works
Self-citationInduction of Cellular p53 Activity by DNA-Damaging Agents and Growth Arrest
Zhan, Q., Carrier, F., & Fornace, A. J. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.7.4242-4250.1993 · Cited by 44 · see citing works
Specific Saccharomyces cerevisiae Genes Are Expressed in Response to DNA-Damaging Agents
Ruby, S. W., & Szostak, J. W. (1985) · Molecular and Cellular Biology · doi:10.1128/mcb.5.1.75-84.1985 · Cited by 41 · see citing works
Specific Transcripts Are Elevated in Saccharomyces cerevisiae in Response to DNA Damage
McClanahan, T. K., & McEntee, K. (1984) · Molecular and Cellular Biology · doi:10.1128/mcb.4.11.2356-2363.1984 · Cited by 38 · see citing works
Role of UME6 in Transcriptional Regulation of a DNA Repair Gene in Saccharomyces cerevisiae
Sweet, D. H., Jang, Y. K., & Sancar, G. B. (1997) · Molecular and Cellular Biology · doi:10.1128/mcb.17.11.6223 · Cited by 35 · see citing works
Methylating agents: their target amino acids in nuclear proteins
Boffa, L. C., & Bolognesi, C. (1985) · Carcinogenesis · doi:10.1093/carcin/6.9.1399 · Cited by 25 · see citing works
Xiao, W., Singh, K. K., Chen, B., & Samson, L. D. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.12.7213-7221.1993 · Cited by 14 · see citing works
Self-citation
Flagged first, then by citations
1 of the 36 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
The DNA damage response: putting checkpoints in perspective
Zhou, B.-B. S., & Elledge, S. J. (2000) · Nature · doi:10.1038/35044005 · Cited by 3,213 · see citing works
Transcriptional Regulatory Networks in <i>Saccharomyces cerevisiae</i>
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) · Science · doi:10.1126/science.1075090 · Cited by 2,956 · see citing works
Coordinated plant defense responses in Arabidopsis revealed by microarray analysis
Schenk, P. M., Kazan, K., Wilson, I. W., Anderson, J. P., Richmond, T., Somerville, S. C., & Manners, J. M. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.21.11655 · Cited by 1,370 · see citing works
Remodeling of Yeast Genome Expression in Response to Environmental Changes
Causton, H. C., Ren, B., Koh, S. S., Harbison, C. T., Kanin, E. I., Jennings, E. G., Lee, T. I., True, H. L., Lander, E. S., & Young, R. A. (2001) · Molecular Biology of the Cell · doi:10.1091/mbc.12.2.323 · Cited by 1,364 · see citing works
Global transcriptional responses of fission yeast to environmental stress
Chen, D., Toone, W. M., Mata, J., Lyne, R., Burns, G., Kivinen, K., Brazma, A., Jones, N., & Bähler, J. (2003) · Molecular Biology of the Cell · doi:10.1091/mbc.e02-08-0499 · Cited by 796 · see citing works
Natarajan, K., Meyer, M. R., Jackson, B. M., Slade, D., Roberts, C., Hinnebusch, A. G., & Marton, M. J. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.13.4347-4368.2001 · Cited by 749 · see citing works
Relating Whole-Genome Expression Data with Protein-Protein InteractionsPreprint
Jansen, R., Greenbaum, D. S., & Gerstein, M. (2002) · Genome Research · doi:10.1101/gr.205602 · Cited by 657 · see citing works
van Attikum, H., Fritsch, O., Höhn, B., & Gasser, S. M. (2004) · Cell · doi:10.1016/j.cell.2004.11.033 · Cited by 609 · see citing works
Identification of additional genes belonging to the LexA regulon in Escherichia coli
de Henestrosa, A. R. F., Ogi, T., Aoyagi, S., Chafin, D. R., Hayes, J. J., Ohmori, H., & Woodgate, R. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.01826.x · Cited by 566 · see citing works
Surviving the Breakup: The DNA Damage Checkpoint
Harrison, J. C., & Haber, J. E. (2006) · Annual Review of Genetics · doi:10.1146/annurev.genet.40.051206.105231 · Cited by 550 · see citing works
Gasch, A. P., Huang, M., Metzner, S., Botstein, D., Elledge, S. J., & Brown, P. O. (2001) · Molecular Biology of the Cell · doi:10.1091/mbc.12.10.2987 · Cited by 542 · see citing works
RESPONSE Re: Markers of DNA Repair and Susceptibility to Cancer in Humans: an Epidemiologic Review
Berwick, M. (2000) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/92.18.1537 · Cited by 545 · see citing works
Verma, R., Chen, S., Feldman, R. M. R., Schieltz, D. M., Yates, J. R., Dohmen, R. J., & Deshaies, R. J. (2000) · Molecular Biology of the Cell · doi:10.1091/mbc.11.10.3425 · Cited by 540 · see citing works
Pomposiello, P. J., Bennik, M. H. J., & Demple, B. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.13.3890-3902.2001 · Cited by 487 · see citing works
Widespread aneuploidy revealed by DNA microarray expression profiling
Hughes, T. R., Roberts, C. J., Dai, H. A., Jones, A. R., Meyer, M. R., Slade, D., Burchard, J., Dow, S., Ward, T. R., Kidd, M. J., et al. (2000) · Nature Genetics · doi:10.1038/77116 · Cited by 482 · see citing works
The use and analysis of microarray data
Butte, A. J. (2002) · Nature Reviews Drug Discovery · doi:10.1038/nrd961 · Cited by 482 · see citing works
Expression Profiling in the Muscular Dystrophies
Chen, Y., Zhao, P., Borup, R., & Hoffman, E. P. (2000) · The Journal of Cell Biology · doi:10.1083/jcb.151.6.1321 · Cited by 481 · see citing works
The genomics of yeast responses to environmental stress and starvation
Gasch, A. P., & Werner‐Washburne, M. (2002) · Functional & Integrative Genomics · doi:10.1007/s10142-002-0058-2 · Cited by 448 · see citing works
Integrated Analysis of Transcriptomic and Proteomic Data
Haider, S., & Pal, R. (2013) · Current Genomics · doi:10.2174/1389202911314020003 · Cited by 432 · see citing works
The Transcriptional Response of Yeast to Saline Stress
Posas, F., Chambers, J. R., Heyman, J. A., Hoeffler, J. P., de Nadal, E., & Ariño, J. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m910016199 · Cited by 423 · see citing works
Functional Specificity among Ribosomal Proteins Regulates Gene Expression
Komili, S., Farny, N. G., Roth, F. P., & Silver, P. A. (2007) · Cell · doi:10.1016/j.cell.2007.08.037 · Cited by 390 · see citing works
Aardema, M. J., & MacGregor, J. T. (2002) · Mutation research. Fundamental and molecular mechanisms of mutagenesis · doi:10.1016/s0027-5107(01)00292-5 · Cited by 390 · see citing works
Hinnebusch, A. G., & Natarajan, K. (2002) · Eukaryotic Cell · doi:10.1128/ec.01.1.22-32.2002 · Cited by 383 · see citing works
Mechanisms and Regulation of Mitotic Recombination in Saccharomyces cerevisiae
Symington, L., Rothstein, R., & Lisby, M. (2014) · Genetics · doi:10.1534/genetics.114.166140 · Cited by 331 · see citing works
Genes required for ionizing radiation resistance in yeast
Bennett, C. B., Lewis, L. K., Karthikeyan, G., Lobachev, K. S., Jin, Y. H., Sterling, J. F., Snipe, J. R., & Resnick, M. A. (2001) · Nature Genetics · doi:10.1038/ng778 · Cited by 328 · see citing works
Trm9-Catalyzed tRNA Modifications Link Translation to the DNA Damage Response
Begley, U., Dyavaiah, M., Patil, A., Rooney, J. P., DiRenzo, D. M., Young, C. M., Conklin, D. S., Zitomer, R. S., & Begley, T. J. (2007) · Molecular Cell · doi:10.1016/j.molcel.2007.09.021 · Cited by 325 · see citing works
Jelinsky, S. A., Estep, P., Church, G. M., & Samson, L. D. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.21.8157-8167.2000 · Cited by 335 · see citing works
Self-citationElucidating mechanisms of drug-induced toxicity
Liebler, D. C., & Guengerich, F. P. (2005) · Nature Reviews Drug Discovery · doi:10.1038/nrd1720 · Cited by 324 · see citing works
Glutathione, Altruistic Metabolite in Fungi
Pócsi, I., Prade, R. A., & Penninckx, M. J. (2004) · Advances in microbial physiology/Advances in Microbial Physiology · doi:10.1016/s0065-2911(04)49001-8 · Cited by 311 · see citing works
Chang, M., Bellaoui, M., Boone, C. M., & Brown, G. W. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.262669299 · Cited by 295 · see citing works
Monitoring gene expression using DNA microarrays
Harrington, C. A., Rosenow, C., & Retief, J. (2000) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(00)00091-6 · Cited by 289 · see citing works
What is Bioinformatics? A Proposed Definition and Overview of the Field
Luscombe, N. M., Greenbaum, D., & Gerstein, M. (2001) · Methods of Information in Medicine · doi:10.1055/s-0038-1634431 · Cited by 453 · see citing works
A Systems Approach to Mapping DNA Damage Response Pathways
Workman, C. T., Mak, H. C., McCuine, S., Tagne, J., Agarwal, M., Ozier, O. W., Begley, T. J., Samson, L. D., & Ideker, T. E. (2006) · Science · doi:10.1126/science.1122088 · Cited by 268 · see citing works
Self-citationBirrell, G. W., Brown, J. A. L., Wu, H. I., Giaever, G. N., Chu, A. M., Davis, R. W., & Brown, J. M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.132275199 · Cited by 255 · see citing works
In Vitro Assembly and Recognition of Lys-63 Polyubiquitin Chains
Hofmann, R. M., & Pickart, C. M. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m103378200 · Cited by 253 · see citing works
Distinct Physiological Functions of Thiol Peroxidase Isoenzymes in Saccharomyces cerevisiae
Park, S. G., Cha, M., Jeong, W., & Kim, I.-H. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.275.8.5723 · Cited by 244 · see citing works
Protein Damage by Reactive Electrophiles: Targets and Consequences
Liebler, D. C. (2007) · Chemical Research in Toxicology · doi:10.1021/tx700235t · Cited by 235 · see citing works
An overview on glutathione in versus non-conventional yeasts
Penninckx, M. J. (2002) · FEMS Yeast Research · doi:10.1016/s1567-1356(02)00081-8 · Cited by 235 · see citing works
Over 1000 genes are involved in the DNA damage response of Escherichia coli
Khil, P. P., & Camerini‐Otero, R. D. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.02878.x · Cited by 234 · see citing works
Shamji, A. F., Kuruvilla, F. G., & Schreiber, S. L. (2000) · Current Biology · doi:10.1016/s0960-9822(00)00866-6 · Cited by 234 · see citing works
Genome-wide expression analyses: Metabolic adaptation of to high sugar stress
Erasmus, D. J., VANDERMERWE, G., & VANVUUREN, H. (2003) · FEMS Yeast Research · doi:10.1016/s1567-1356(02)00203-9 · Cited by 232 · see citing works
Lovejoy, K. S., & Lippard, S. J. (2009) · Dalton Transactions · doi:10.1039/b913896j · Cited by 230 · see citing works
Gene Expression Profile of Campylobacter jejuni in Response to Growth Temperature Variation
Stintzi, A. P. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.6.2009-2016.2003 · Cited by 230 · see citing works
Transcript Expression in Saccharomyces cerevisiae at High Salinity
Yale, J., & Bohnert, H. J. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m008209200 · Cited by 226 · see citing works
Hollis, T., Ichikawa, Y., & Ellenberger, T. (2000) · The EMBO Journal · doi:10.1093/emboj/19.4.758 · Cited by 222 · see citing works
A question of size: the eukaryotic proteome and the problems in defining it
Harrison, P. M. (2002) · Nucleic Acids Research · doi:10.1093/nar/30.5.1083 · Cited by 222 · see citing works
Bammert, G. F., & Fostel, J. M. (2000) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.44.5.1255-1265.2000 · Cited by 213 · see citing works
Global Transcriptome Analysis of the Heat Shock Response of Shewanella oneidensis
Gao, H., Wang, Y., Liu, X., Yan, T., Wu, L., Alm, E. J., Arkin, A. P., Thompson, D. K., & Zhou, J. Z. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.22.7796-7803.2004 · Cited by 203 · see citing works
Blomberg, A. (2000) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2000.tb08864.x · Cited by 198 · see citing works
Blaiseau, P.-L., Lesuisse, E., & Camadro, J. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m104987200 · Cited by 193 · see citing works
Greenbaum, D. S., Jansen, R., & Gerstein, M. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.4.585 · Cited by 183 · see citing works
A transmembrane ubiquitin ligase required to sort membrane proteins into multivesicular bodies
Reggiori, F., & Pelham, H. R. B. (2002) · Nature Cell Biology · doi:10.1038/ncb743 · Cited by 179 · see citing works
Sahara, T., Goda, T., & Ohgiya, S. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m209258200 · Cited by 176 · see citing works
Cavalieri, D., Townsend, J. P., & Hartl, D. L. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.210395297 · Cited by 174 · see citing works
Yan, L. L., & Zaher, H. S. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.11.033 · Cited by 173 · see citing works
Krogan, N. J., & Greenblatt, J. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.23.8203-8212.2001 · Cited by 170 · see citing works
Integrating stress-response and cell-cycle checkpoint pathways
Pearce, A. K., & Humphrey, T. C. (2001) · Trends in Cell Biology · doi:10.1016/s0962-8924(01)02119-5 · Cited by 167 · see citing works
von der Haar, T. (2008) · BMC Systems Biology · doi:10.1186/1752-0509-2-87 · Cited by 163 · see citing works
Begley, T. J., Rosenbach, A., Ideker, T. E., & Samson, L. D. (2002) · PubMed · Cited by 163 · see citing works
Self-citationJansen, R. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg306 · Cited by 161 · see citing works
Brusky, J., Zhu, Y. B., & Xiao, W. (2000) · Current Genetics · doi:10.1007/s002940050515 · Cited by 157 · see citing works
Ybp1 Is Required for the Hydrogen Peroxide-induced Oxidation of the Yap1 Transcription Factor
Veal, E. A., Ross, S. J., Malakasi, P., Peacock, E., & Morgan, B. A. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m303542200 · Cited by 156 · see citing works
General Statistics of Stochastic Process of Gene Expression in Eukaryotic Cells
Kuznetsov, V. A., Knott, G. D., & Bonner, R. F. (2002) · Genetics · doi:10.1093/genetics/161.3.1321 · Cited by 151 · see citing works
Jansen, R. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.6.1481 · Cited by 149 · see citing works
Rosenfeld, E., & Beauvoit, B. (2003) · Yeast · doi:10.1002/yea.1026 · Cited by 149 · see citing works
Silber, J. R., Bobola, M. S., Blank, A., Schoeler, K. D., Haroldson, P. D., Huynh, M. B., & Kolstoe, D. D. (2002) · PubMed · Cited by 149 · see citing works
Momose, Y., & Iwahashi, H. (2001) · Environmental Toxicology and Chemistry · doi:10.1002/etc.5620201030 · Cited by 145 · see citing works
Microarray technology — enhanced versatility, persistent challenge
Epstein, C. B. (2000) · Current Opinion in Biotechnology · doi:10.1016/s0958-1669(99)00065-8 · Cited by 139 · see citing works
SUMO-2 Orchestrates Chromatin Modifiers in Response to DNA Damage
Hendriks, I. A., Treffers, L. W., Vries, M. V., Olsen, J. V., & Vertegaal, A. C. O. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.02.033 · Cited by 136 · see citing works
What is bioinformatics? An introduction and overview
Luscombe, N. M., Greenbaum, D. S., & Gerstein, M. (2001) · Yearbook of Medical Informatics · doi:10.1055/s-0038-1638103 · Cited by 136 · see citing works
Possible regulatory function of the Saccharomyces cerevisiae Ty1 retrotransposon core protein
Roth, J., Kingsman, S., Kingsman, A., & Martin-Rendon, E. (2000) · Yeast · doi:10.1002/1097-0061(200007)16:10
Holtorf, H., Guitton, M.-C., & Ralf Reski, A. (2002) · Die Naturwissenschaften · doi:10.1007/s00114-002-0321-3 · Cited by 133 · see citing works
Two redox centers within Yap1 for H2O2 and thiol-reactive chemicals signaling
Azevedo, D., Tacnet, F., Delaunay, A., Rodrigues‐Pousada, C., & Tolédano, M. B. (2003) · Free Radical Biology and Medicine · doi:10.1016/s0891-5849(03)00434-9 · Cited by 133 · see citing works
Unique Gene Expression Patterns in Liver and Kidney Associated with Exposure to Chemical Toxicants
Bartosiewicz, M. J., Jenkins, D., Penn, S. G., Emery, J., & Buckpitt, A. R. (2001) · Journal of Pharmacology and Experimental Therapeutics · doi:10.1016/s0022-3565(24)29613-0 · Cited by 133 · see citing works
Regulation of ribosome biogenesis within the nucleolus
Leary, D. J., & Huang, S. (2001) · FEBS Letters · doi:10.1016/s0014-5793(01)03143-x · Cited by 132 · see citing works
Ghavidel, A., & Schultz, M. C. (2001) · Cell · doi:10.1016/s0092-8674(01)00473-1 · Cited by 131 · see citing works
Use of Transcriptomics in Understanding Mechanisms of Drug-Induced Toxicity
Cui, Y., & Paules, R. S. (2010) · Pharmacogenomics · doi:10.2217/pgs.10.37 · Cited by 130 · see citing works
Microarrays for microbiologists
Lucchini, S., Thompson, A., & Hinton, J. C. D. (2001) · Microbiology · doi:10.1099/00221287-147-6-1403 · Cited by 130 · see citing works
DNA replication as a target of the DNA damage checkpoint
Zegerman, P., & Diffley, J. F. X. (2009) · DNA Repair · doi:10.1016/j.dnarep.2009.04.023 · Cited by 128 · see citing works
Said, M. R., Begley, T. J., Oppenheim, A. V., Lauffenburger, D. A., & Samson, L. D. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0405996101 · Cited by 121 · see citing works
Self-citationJia, M. H., LaRossa, R. A., Lee, J.-M., Rafalski, A. J., DeRose, E. J., Gonye, G., & Xue, Z. (2000) · Physiological Genomics · doi:10.1152/physiolgenomics.2000.3.2.83 · Cited by 127 · see citing works
Transcription, genomes, function
Cho, R. J., & Campbell, M. J. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(00)02065-5 · Cited by 126 · see citing works
Differential global gene expression in red and white skeletal muscle
Campbell, W. G., Gordon, S. E., Carlson, C. J., Pattison, J. S., Hamilton, M. T., & Booth, F. W. (2001) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.2001.280.4.c763 · Cited by 126 · see citing works
The environmental stress response: a common yeast response to diverse environmental stresses
Gasch, A. P. (2007) · Springer eBooks · doi:10.1007/3-540-45611-2_2 · Cited by 125 · see citing works
The Transcriptome of Prematurely Aging Yeast Cells Is Similar to That of Telomerase-deficient Cells
Lesur, I., & Campbell, J. L. (2004) · Molecular Biology of the Cell · doi:10.1091/mbc.e03-10-0742 · Cited by 123 · see citing works
Identification of gene expression patterns in superficial and invasive human bladder cancer.
Thykjær, T., Workman, C. T., Kruhøffer, M., Demtröder, K., Wolf, H., Andersen, L. D., Frederiksen, C. M., Knudsen, S., & Orntoft, T. F. (2001) · PubMed · Cited by 119 · see citing works
de Nobel, H., Lawrie, L. C., Brul, S., Klis, F. M., Davis, M. A. F., Alloush, H. M., & Coote, P. J. (2001) · Yeast · doi:10.1002/yea.793 · Cited by 118 · see citing works
Cui, L., Miao, J., Furuya, T., Fan, Q., Li, X., Rathod, P. K., Su, X., & Cui, L. (2008) · Eukaryotic Cell · doi:10.1128/ec.00063-08 · Cited by 112 · see citing works
The role of glutathione transferases in cadmium stress
Adamis, P. D. B., Gomes, D. S., Pinto, M. L. C. C., Panek, A. D., & Eleuthério, E. C. A. (2004) · Toxicology Letters · doi:10.1016/j.toxlet.2004.07.003 · Cited by 110 · see citing works
Rimini, R., Jansson, B., Feger, G., Roberts, T. C., Francesco, M. D., Gozzi, A., Faggioni, F., Domenici, E., Wallace, D. M., Frandsen, N., et al. (2000) · Molecular Microbiology · doi:10.1046/j.1365-2958.2000.01931.x · Cited by 110 · see citing works
The utility of DNA microarrays for characterizing genotoxicity.
Newton, R. K., Aardema, M. J., & Aubrecht, J. (2004) · Environmental Health Perspectives · doi:10.1289/ehp.6709 · Cited by 109 · see citing works
Nguyên, D.-T., Alarco, A., & Raymond, M. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m008377200 · Cited by 107 · see citing works
Owsianik, G., Balzi, L., & Ghislain, M. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.02823.x · Cited by 106 · see citing works
Toxicogenomics: a pivotal piece in the puzzle of toxicological research
Gatzidou, E. T., Zira, A. N., & Theocharis, S. E. (2007) · Journal of Applied Toxicology · doi:10.1002/jat.1248 · Cited by 102 · see citing works
Mallory, J. C., Crudden, G., Johnson, B. L., Mo, C., Pierson, C. A., Bard, M., & Craven, R. J. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.5.1669-1679.2005 · Cited by 102 · see citing works
Kaplun, L., Tzirkin, R., Bakhrat, A., Shabek, N., Ivantsiv, Y., & Raveh, D. (2005) · Molecular and Cellular Biology · doi:10.1128/mcb.25.13.5355-5362.2005 · Cited by 101 · see citing works
Cunningham, M. J. (2000) · Journal of Pharmacological and Toxicological Methods · doi:10.1016/s1056-8719(00)00111-8 · Cited by 101 · see citing works
Emerging technologies in yeast genomics
Kumar, A., & Snyder, M. P. (2001) · Nature Reviews Genetics · doi:10.1038/35066084 · Cited by 100 · see citing works
Molin, M., Norbeck, J., & Blomberg, A. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m203030200 · Cited by 99 · see citing works
The genome-wide expression response to telomerase deletion in <i>Saccharomyces</i> <i>cerevisiae</i>
Nautiyal, S., DeRisi, J. L., & Blackburn, E. H. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.142162499 · Cited by 96 · see citing works
- Authors
- Jelinsky, S. A., & Samson, L. D.
- Affiliations
- Harvard University (US)
- Corresponding author
- Samson, Leona D.
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 1999-02-16
- Volume
- 96
- Issue
- 4
- Pages
- 1486-1491
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC15489
- OpenAlex
- W2155675863
- Cited by
- 419
- References
- 36
- Citations by year
- 2026: 4 · 2025: 1 · 2024: 4 · 2023: 4 · 2022: 2 · 2021: 1 · 2020: 5 · 2019: 6 · 2018: 6 · 2017: 4 · 2016: 5 · 2015: 11 · 2014: 10 · 2013: 8 · 2012: 11
- FWCI
- 17.46
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health (5p01hg001323-03)
- National Human Genome Research Institute (P01 HG 01323)
- National Cancer Institute (CA-55042, CA09078, T32CA009078, R01CA055042)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- Saccharomyces cerevisiae, methyl methanesulfonate, alkylating agents, DNA damage response, gene expression profiling, transcriptome, DNA repair genes
- MeSH terms
- Alkylating Agents, DNA Damage, Fungal Proteins, Genes, Fungal, Methyl Methanesulfonate, Saccharomyces cerevisiae, Transcription, Genetic, Open Reading Frames, Genome, Fungal
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review