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2. Proposed changes for NIH's Center for Scientific Review. Panel on Scientific Boundaries for Review. Center for Scientific Review Advisory Committee, National Institutes of Health.

Author

Alberts, BM, Ayala, FJ, Botstein, D, Frank, E, Holmes, EW, Lee, RD, Macagno, ER, Marrack, P, Oparil, S, Orkin, SH, Rubenstein, AH, Slayman, CW, Sparling, PF, Squire, LR, von Hippel, PH, and Yamamoto, KR

Subjects
Peer Review, Research, Research, National Institutes of Health (U.S.), Public Policy, United States, Peer Review, National Institutes of Health, General Science & Technology
Published
1999

5. Genome-wide scan of bipolar disorder in 65 pedigrees: supportive evidence for linkage at 8q24, 18q22, 4q32, 2p12, and 13q12

Author

McInnis, M G, Lan, T-H, Willour, V L, McMahon, F J, Simpson, S G, Addington, A M, MacKinnon, D F, Potash, J B, Mahoney, A T, Chellis, J, Huo, Y, Swift-Scanlan, T, Chen, H, Koskela, R, Colin Stine, O, Jamison, K R, Holmans, P, Folstein, S E, Ranade, K, Friddle, C, Botstein, D, Marr, T, Beaty, T H, Zandi, P, and Raymond DePaulo, J

Published
2003
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6. The Gene Ontology in 2010: extensions and refinements

Author

Berardini, Tz, Li, D, Huala, E, Bridges, S, Burgess, S, Mccarthy, F, Carbon, S, Lewis, Se, Mungall, Cj, Abdulla, A, Wood, V, Feltrin, E, Valle, Giorgio, Chisholm, Rl, Fey, P, Gaudet, P, Kibbe, W, Basu, S, Bushmanova, Y, Eilbeck, K, Siegele, Da, Mcintosh, B, Renfro, D, Zweifel, A, Hu, Jc, Ashburner, M, Tweedie, S, ALAM FARUQUE, Y, Apweiler, R, Auchinchloss, A, Bairoch, A, Barrell, D, Binns, D, Blatter, Mc, Bougueleret, L, Boutet, E, Breuza, L, Bridge, A, Browne, P, Chan, Wm, Coudert, E, Daugherty, L, Dimmer, E, Eberhardt, R, Estreicher, A, Famiglietti, L, FERRO ROJAS, S, Feuermann, M, Foulger, R, GRUAZ GUMOWSKI, N, Hinz, U, Huntley, R, Jimenez, S, Jungo, F, Keller, G, Laiho, K, Legge, D, Lemercier, P, Lieberherr, D, Magrane, M, O'Donovan, C, Pedruzzi, I, Poux, S, Rivoire, C, Roechert, B, Sawford, T, Schneider, M, Stanley, E, Stutz, A, Sundaram, S, Tognolli, M, Xenarios, I, Harris, Ma, Deegan, Ji, Ireland, A, Lomax, J, Jaiswal, P, Chibucos, M, Giglio, Mg, Wortman, J, Hannick, L, Madupu, R, Botstein, D, Dolinski, K, Livstone, Ms, Oughtred, R, Blake, Ja, Bult, C, Diehl, Ad, Dolan, M, Drabkin, H, Eppig, Jt, Hill, Dp, Ni, L, Ringwald, M, Sitnikov, D, Collmer, C, TORTO ALALIBO, T, Laulederkind, S, Shimoyama, M, Twigger, S, D'Eustachio, P, Matthews, L, Balakrishnan, R, Binkley, G, Cherry, Jm, Christie, Kr, Costanzo, Mc, Engel, Sr, Fisk, Dg, Hirschman, Je, Hitz, Bc, Hong, El, Krieger, Cj, Miyasato, Sr, Nash, Rs, Park, J, Skrzypek, Ms, Weng, S, Wong, Ed, Aslett, M, Chan, J, Kishore, R, Sternberg, P, VAN AUKE, K, Khodiyar, Vk, Lovering, Rc, Talmud, Pj, Howe, D, Westerfield, M., Gene Ontology Consortium, Berardini, TZ., Li, D., Huala, E., Bridges, S., Burgess, S., McCarthy, F., Carbon, S., Lewis, SE., Mungall, CJ., Abdulla, A., Wood, V., Feltrin, E., Valle, G., Chisholm, RL., Fey, P., Gaudet, P., Kibbe, W., Basu, S., Bushmanova, Y., Eilbeck, K., Siegele, DA., McIntosh, B., Renfro, D., Zweifel, A., Hu, JC., Ashburner, M., Tweedie, S., Alam-Faruque, Y., Apweiler, R., Auchinchloss, A., Bairoch, A., Barrell, D., Binns, D., Blatter, MC., Bougueleret, L., Boutet, E., Breuza, L., Bridge, A., Browne, P., Chan, WM., Coudert, E., Daugherty, L., Dimmer, E., Eberhardt, R., Estreicher, A., Famiglietti, L., Ferro-Rojas, S., Feuermann, M., Foulger, R., Gruaz-Gumowski, N., Hinz, U., Huntley, R., Jimenez, S., Jungo, F., Keller, G., Laiho, K., Legge, D., Lemercier, P., Lieberherr, D., Magrane, M., O'Donovan, C., Pedruzzi, I., Poux, S., Rivoire, C., Roechert, B., Sawford, T., Schneider, M., Stanley, E., Stutz, A., Sundaram, S., Tognolli, M., Xenarios, I., Harris, MA., Deegan, JI., Ireland, A., Lomax, J., Jaiswal, P., Chibucos, M., Giglio, MG., Wortman, J., Hannick, L., Madupu, R., Botstein, D., Dolinski, K., Livstone, MS., Oughtred, R., Blake, JA., Bult, C., Diehl, AD., Dolan, M., Drabkin, H., Eppig, JT., Hill, DP., Ni, L., Ringwald, M., Sitnikov, D., Collmer, C., Torto-Alalibo, T., Laulederkind, S., Shimoyama, M., Twigger, S., D'Eustachio, P., Matthews, L., Balakrishnan, R., Binkley, G., Cherry, JM., Christie, KR., Costanzo, MC., Engel, SR., Fisk, DG., Hirschman, JE., Hitz, BC., Hong, EL., Krieger, CJ., Miyasato, SR., Nash, RS., Park, J., Skrzypek, MS., Weng, S., Wong, ED., Aslett, M., Chan, J., Kishore, R., Sternberg, P., Van Auke, K., Khodiyar, VK., Lovering, RC., Talmud, PJ., Howe, D., and Westerfield, M.

Subjects
Information Storage and Retrieval, Ontology (information science), Biology, Bioinformatics, World Wide Web, Set (abstract data type), 03 medical and health sciences, Annotation, User-Computer Interface, 0302 clinical medicine, Controlled vocabulary, Databases, Genetic, Genetics, Animals, Humans, Databases, Protein, Computational Biology/methods, Computational Biology/trends, Databases, Nucleic Acid, Genomics, Information Storage and Retrieval/methods, Internet, Software, Vocabulary, Controlled, 030304 developmental biology, Structure (mathematical logic), 0303 health sciences, Gene ontology, business.industry, Computational Biology, Usability, Articles, ComputingMethodologies_GENERAL, business, 030217 neurology & neurosurgery
Abstract

The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop, maintain and use a set of structured, controlled vocabularies for the annotation of genes, gene products and sequences. The GO ontologies are expanding both in content and in structure. Several new relationship types have been introduced and used, along with existing relationships, to create links between and within the GO domains. These improve the representation of biology, facilitate querying, and allow GO developers to systematically check for and correct inconsistencies within the GO. Gene product annotation using GO continues to increase both in the number of total annotations and in species coverage. GO tools, such as OBO-Edit, an ontology-editing tool, and AmiGO, the GOC ontology browser, have seen major improvements in functionality, speed and ease of use.

Published
2010

7. The Yeast Genome Directory

Author

Goffeau, A., Aert, R., Agostini-Carbone, M. L., Ahmed, A., Aigle, M., Alberghina, L., Albermann, K., Albers, M., Aldea, M., Alexandraki, D., Aljinovic, G., Allen, E., Alt-Mörbe, J., André, B., Andrews, S., Ansorge, W., Antoine, G., Anwar, R., Aparicio, A., Araujo, R., Arino, J., Arnold, F., Arroyo, J., Aviles, E., Backes, U., Baclet, M. C., Badcock, K., Bahr, A., Baladron, V., Ballesta, J. P. G., Bankier, A. T., Banrevi, A., Bargues, M., Baron, L., Barreiros, T., Barrell, B. G., Barthe, C., Barton, A. B., Baur, A., Bécam, A.-M., Becker, A., Becker, I., Beinhauer, J., Benes, V., Benit, P., Berben, G., Bergantino, E., Bergez, P., Berno, A., Bertani, I., Biteau, N., Bjourson, A. J., Blöcker, H., Blugeon, C., Bohn, C., Boles, E., Bolle, P. A., Bolotin-Fukuhara, M., Bordonné, R., Boskovic, J., Bossier, P., Botstein, D., Bou, G., Bowman, S., Boyer, J., Brandt, P., Brandt, T., Brendel, M., Brennan, T., Brinkman, R., Brown, A., Brown, A. J. P., Brown, D., Brückner, M., Bruschi, C. V., Buhler, J. M., Buitrago, M. J., Bussereau, F., Bussey, H., Camasses, A., Carcano, C., Carignani, G., Carpenter, J., Casamayor, A., Casas, C., Castagnoli, L., Cederberg, H., Cerdan, E., Chalwatzis, N., Chanet, R., Chen, E., Chéret, G., Cherry, J. M., Chillingworth, T., Christiansen, C., Chuat, J.-C., Chung, E., Churcher, C., Churcher, C. M., Clark, M. W., Clemente, M. L., Coblenz, A., Coglievina, M., Coissac, E., Colleaux, L., Connor, R., Contreras, R., Cooper, J., Copsey, T., Coster, F., Coster, R., Couch, J., Crouzet, M., Cziepluch, C., Daignan-Fornier, B., Dal Paro, F., Dang, D. V., D’Angelo, M., Davies, C. J., Davis, K., Davis, R. W., De Antoni, A., Dear, S., Dedman, K., Defoor, E., De Haan, M., Delaveau, Th., Del Bino, S., Delgado, M., Delius, H., Delneri, D., Del Rey, F., Demolder, J., Démolis, N., Devlin, K., de Wergifosse, P., Dietrich, F. S., Ding, H., Dion, C., Dipaolo, T., Doignon, F., Doira, C., Domdey, H., Dover, J., Du, Z., Dubois, E., Dujon, B., Duncan, M., Durand, P., Düsterhöft, A., Düsterhus, S., Eki, T., El Bakkoury, M., Eide, L. G., Entian, K.-D., Eraso, P., Erdmann, D., Erfle, H., Escribano, V., Esteban, M., Fabiani, L., Fabre, F., Fairhead, C., Fartmann, B., Favello, A., Faye, G., Feldmann, H., Fernandes, L., Feroli, F., Feuermann, M., Fiedler, T., Fiers, W., Fleig, U. N., Flöth, M., Fobo, G. M., Fortin, N., Foury, F., Francingues-Gaillard, M. C., Franco, L., Fraser, A., Friesen, J.D., Fritz, C., Frontali, L., Fukuhara, H., Fulton, L., Fuller, L. J., Gabel, C., Gaillardin, C., Gaillon, L., Galibert, F., Galisson, F., Galland, P., Gamo, F.-J., Gancedo, C., Garcia-Cantalejo, J. M., García-Gonzalez, M. I., Garcia-Ramirez, J. J., García-Saéz, M., Gassenhuber, H., Gatius, M., Gattung, S., Geisel, C., Gent, M. E., Gentles, S., Ghazvini, M., Gigot, D., Gilliquet, V., Glansdorff, N., Gómez-Peris, A., Gonzaléz, A., Goulding, S. E., Granotier, C., Greco, T., Grenson, M., Grisanti, P., Grivell, L. A., Grothues, D., Gueldener, U., Guerreiro, P., Guzman, E., Haasemann, M., Habbig, B., Hagiwara, H., Hall, J., Hallsworth, K., Hamlin, N., Hand, N. J., Hanemann, V., Hani, J., Hankeln, T., Hansen, M., Harris, D., Harris, D. E., Hartzell, G., Hatat, D., Hattenhorst, U., Hawkins, J., Hebling, U., Hegemann, J., Hein, C., Hennemann, A., Hennessy, K., Herbert, C. J., Hernandez, K., Hernando, Y., Herrero, E., Heumann, K., Heuss- Neitzel, D., Hewitt, N., Hiesel, R., Hilbert, H., Hilger, F., Hillier, L., Ho, C., Hoenicka, J., Hofmann, B., Hoheisel, J., Hohmann, S., Hollenberg, C. P., Holmstrøm, K., Horaitis, O., Horsnell, T. S., Huang, M.-E., Hughes, B., Hunicke-Smith, S., Hunt, S., Hunt, S. E., Huse, K., Hyman, R. W., Iborra, F., Indge, K. J., Iraqui Houssaini, I., Isono, K., Jacq, C., Jacquet, M., Jacquier, A., Jagels, K., Jäger, W., James, C. M., Jauniaux, J. C., Jia, Y., Jier, M., Jimenez, A., Johnson, D., Johnston, L., Johnston, M., Jones, M., Jonniaux, J.-L., Kaback, D. B., Kallesøe, T., Kalman, S., Kalogeropoulos, A., Karpfinger-Hartl, L., Kashkari, D., Katsoulou, C., Kayser, A., Kelly, A., Keng, T., Keuchel, H., Kiesau, P., Kirchrath, L., Kirsten, J., Kleine, K., Kleinhans, U., Klima, R., Komp, C., Kordes, E., Korol, S., Kötter, P., Krämer, C., Kramer, B., Kreisl, P., Kucaba, T., Kuester, H., Kurdi, O., Laamanen, P., Lafuente, M. J., Landt, O., Lanfranchi, G., Langston, Y., Lashkari, D., Latreille, P., Lauquin, G., Le, T., Legrain, P., Legros, Y., Lepingle, A., Lesveque, H., Leuther, H., Lew, H., Lewis, C., Li, Z. Y., Liebl, S., Lin, A., Lin, D., Logghe, M., Lohan, A. J. E., Louis, E. J., Lucchini, G., Lutzenkirchen, K., Lyck, R., Lye, G., Maarse, A. C., Maat, M. J., Macri, C., Madania, A., Maftahi, M., Maia e Silva, A., Maillier, E., Mallet, L., Mannhaupt, G., Manus, V., Marathe, R., Marck, C., Marconi, A., Mardis, E., Martegani, E., Martin, R., Mathieu, A., Maurer, C. T. C., Mazón, M. J., Mazzoni, C., McConnell, D., McDonald, S., McKee, R. A., McReynolds, A. D. K., Melchioretto, P., Menezes, S., Messenguy, F., Mewes, H. W., Michaux, G., Miller, N., Minenkova, O., Miosga, T., Mirtipati, S., Möller-Rieker, S., Möstl, D., Molemans, F., Monnet, A., Monnier, A-L., Montague, M. A., Moro, M., Mosedale, D., Möstl, D., Moule, S., Mouser, L., Murakami, Y., Müller-Auer, S., Mulligan, J., Murphy, L., Muzi Falconi, M., Naitou, M., Nakahara, K., Namath, A., Nasr, F., Navas, L., Nawrocki, A., Nelson, J., Nentwich, U., Netter, P., Neu, R., Newlon, C. S., Nhan, M., Nicaud, J.-M., Niedenthal, R. K., Nombela, C., Noone, D., Norgren, R., Nußbaumer, B., Obermaier, B., Odell, C., Öfner, P., Oh, C., Oliver, K., Oliver, S. G., Ouellette, B. F., Ozawa, M., Paces, V., Pallier, C., Pandolfo, D., Panzeri, L., Paoluzi, S., Parle-Mcdermott, A. G., Pascolo, S., Patricio, N., Pauley, A., Paulin, L., Pearson, B. M., Pearson, D., Peluso, D., Perea, J., Pérez-Alonso, M., Pérez-Ortin, J. E., Perrin, A., Petel, F. X., Pettersson, B., Pfeiffer, F., Philippsen, P., Piérard, A., Piravandi, E., Planta, R. J., Plevani, P., Poch, O., Poetsch, B., Pohl, F. M., Pohl, T. M., Pöhlmann, R., Poirey, R., Portetelle, D., Portillo, F., Potier, S., Proft, M., Prydz, H., Pujol, A., Purnelle, B., Puzos, V., Rajandream, M. A., Ramezani Rad, M., Rasmussen, S. W., Raynal, A., Rechmann, S., Remacha, M., Revuelta, J. L., Rice, P., Richard, G-F., Richterich, P., Rieger, M., Rifken, L., Riles, L., Rinaldi, T., Rinke, M., Roberts, A. B., Roberts, D., Rodriguez, F., Rodriguez-Belmonte, E., Rodriguez-Pousada, C., Rodriguez-Torres, A. M., Rose, M., Rossau, R., Rowley, N., Rupp, T., Ruzzi, M., Saeger, W., Saiz, J. E., Saliola, M., Salom, D., Saluz, H. P., Sánchez-Perez, M., Santos, M. A., Sanz, E., Sanz, J. E., Saren, A.-M., Sartorello, F., Sasanuma, M., Sasanuma, S-I., Scarcez, T., Schaaf-Gerstenschläger, I., Schäfer, B., Schäfer, M., Scharfe, M., Scherens, B., Schroff, N., Sen-Gupta, M., Shibata, T., Schmidheini, T., Schmidt, E. R., Schneider, C., Scholler, P., Schramm, S., Schreer, A., Schröder, M., Schwager, C., Schwarz, S., Schwarzlose, C., Schweitzer, B., Schweizer, M., Sdicu, A-M., Sehl, P., Sensen, C., Sgouros, J. G., Shogren, T., Shore, L., Shu, Y., Skala, J., Skelton, J., Slonimski, P. P., Smit, P. H. M., Smith, V., Soares, H., Soeda, E., Soler-Mira, A., Sor, F., Soriano, N., Souciet, J. L., Soustelle, C., Spiegelberg, R., Stateva, L. I., Steensma, H. Y., Stegemann, J., Steiner, S., Stellyes, L., Sterky, F., Storms, R. K., St. Peter, H., Stucka, R., Taich, A., Talla, E., Tarassov, I., Tashiro, H., Taylor, P., Teodoru, C., Tettelin, H., Thierry, A., Thireos, G., Tobiasch, E., Tovan, D., Trevaskis, E., Tsuchiya, Y., Tzermia, M., Uhlen, M., Underwood, A., Unseld, M., Urbanus, J. H. M., Urrestarazu, A., Ushinsky, S., Valens, M., Valle, G., Van Broekhoven, A., Vandenbol, M., Van Der Aart, Q. J. M., Van Der Linden, C. G., Van Dyck, L., Vanoni, M., Van Vliet-Reedijk, J. C., Vassarotti, A., Vaudin, M., Vaughan, K., Verhasselt, P., Vetter, I., Vierendeels, F., Vignati, D., Vilela, C., Vissers, S., Vleck, C., Vo, D. T., Vo, D. H., Voet, M., Volckaert, G., Von Wettstein, D., Voss, H., Vreken, P., Wagner, G., Walsh, S. V., Wambutt, R., Wang, H., Wang, Y., Warmington, J. R., Waterston, R., Watson, M. D., Weber, N., Wedler, E., Wedler, H., Wei, Y., Whitehead, S., Wicksteed, B. L., Wiemann, S., Wilcox, L., Wilson, C., Wilson, R., Winant, A., Winnett, E., Winsor, B., Wipfli, P., Wölfl, S., Wohldman, P., Wolf, K., Wolfe, K. H., Wright, L. F., Wurst, H., Xu, G., Yamasaki, M., Yelton, M. A., Yokohama, K., Yoshikawa, A., Yuping, S., Zaccaria, P., Zagulski, M., Zimmermann, F. K., Zimmermann, J., Zimmermann, M., Zhong, W-W., Zollner, A., and Zumstein, E.

Published
1997
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9. The nucleotide sequence of Saccharomyces cerevisiae chromosome V

Author

Dietrich, F. S., Mulligan, J., Hennessy, K., Yelton, M. A., Allen, E., Araujo, R., Aviles, E., Berno, A., Brennan, T., Carpenter, J., Chen, E., Cherry, J. M., Chung, E., Duncan, M., Guzman, E., Hartzell, G., Hunicke-Smith, S., Hyman, R. W., Kayser, A., Komp, C., Lashkari, D., Lew, H., Lin, D., Mosedale, D., Nakahara, K., Namath, A., Norgren, R., Oefner, P., Oh, C., Petel, F. X., Roberts, D., Sehl, P., Schramm, S., Shogren, T., Smith, V., Taylor, P., Wei, Y., Botstein, D., and Davis, R. W.

Subjects
Multidisciplinary, Base Sequence, Molecular Sequence Data, Saccharomyces cerevisiae, Chromosomes, Fungal, DNA, Fungal, Article
Abstract

Here we report the sequence of 569,202 base pairs of Saccharomyces cerevisiae chromosome V. Analysis of the sequence revealed a centromere, two telomeres and 271 open reading frames (ORFs) plus 13 tRNAs and four small nuclear RNAs. There are two Tyl transposable elements, each of which contains an ORF (included in the count of 271). Of the ORFs, 78 (29%) are new, 81 (30%) have potential homologues in the public databases, and 112 (41%) are previously characterized yeast genes.

Published
1997

10. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors

Author

Botstein, D., Lonning, P. E., Tibshirani, R., Borresen-Dale, A.-L., Perou, C. M., Brown, P. O., Pollack, J. R., Jeffrey, S. S., Rees, C. A., and Sorlie, T.

Abstract

Genomic DNA copy number alterations are key genetic events in the development and progression of human cancers. Here we report a genome-wide microarray comparative genomic hybridization (array CGH) analysis of DNA copy number variation in a series of primary human breast tumors. We have profiled DNA copy number alteration across 6,691 mapped human genes, in 44 predominantly advanced, primary breast tumors and 10 breast cancer cell lines. While the overall patterns of DNA amplification and deletion corroborate previous cytogenetic studies, the high-resolution (gene-by-gene) mapping of amplicon boundaries and the quantitative analysis of amplicon shape provide significant improvement in the localization of candidate oncogenes. Parallel microarray measurements of mRNA levels reveal the remarkable degree to which variation in gene copy number contributes to variation in gene expression in tumor cells. Specifically, we find that 62% of highly amplified genes show moderately or highly elevated expression, that DNA copy number influences gene expression across a wide range of DNA copy number alterations (deletion, low-, mid- and high-level amplification), that on average, a 2-fold change in DNA copy number is associated with a corresponding 1.5-fold change in mRNA levels, and that overall, at least 12% of all the variation in gene expression among the breast tumors is directly attributable to underlying variation in gene copy number. These findings provide evidence that widespread DNA copy number alteration can lead directly to global deregulation of gene expression, which may contribute to the development or progression of cancer.

Published
2002
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11. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications

Author

Matese, J. C., Sorlie, T., Tibshirani, R., Jeffrey, S. S., Johnsen, H., Brown, P. O., Lonning, P. E., Quist, H., Botstein, D., Eisen, M. B., Borresen-Dale, A.-L., Hastie, T., Geisler, S., van de Rijn, M., Aas, T., Thorsen, T., and Perou, C. M.

Abstract

The purpose of this study was to classify breast carcinomas based on variations in gene expression patterns derived from cDNA microarrays and to correlate tumor characteristics to clinical outcome. A total of 85 cDNA microarray experiments representing 78 cancers, three fibroadenomas, and four normal breast tissues were analyzed by hierarchical clustering. As reported previously, the cancers could be classified into a basal epithelial-like group, an ERBB2-overexpressing group and a normal breast-like group based on variations in gene expression. A novel finding was that the previously characterized luminal epithelial/estrogen receptor-positive group could be divided into at least two subgroups, each with a distinctive expression profile. These subtypes proved to be reasonably robust by clustering using two different gene sets: first, a set of 456 cDNA clones previously selected to reflect intrinsic properties of the tumors and, second, a gene set that highly correlated with patient outcome. Survival analyses on a subcohort of patients with locally advanced breast cancer uniformly treated in a prospective study showed significantly different outcomes for the patients belonging to the various groups, including a poor prognosis for the basal-like subtype and a significant difference in outcome for the two estrogen receptor-positive groups.

Published
2001
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12. A conserved cell growth cycle can account for the environmental stress responses of divergent eukaryotes

Author

Slavov, N., Airoldi, E.M., van Oudenaarden, A., Botstein, D., Slavov, N., Airoldi, E.M., van Oudenaarden, A., and Botstein, D.

Abstract

The respiratory metabolic cycle in budding yeast (Saccharomyces cerevisiae) consists of two phases that are most simply defined phenomenologically: low oxygen consumption (LOC) and high oxygen consumption (HOC). Each phase is associated with the periodic expression of thousands of genes, producing oscillating patterns of gene expression found in synchronized cultures and in single cells of slowly growing unsynchronized cultures. Systematic variation in the durations of the HOC and LOC phases can account quantitatively for well-studied transcriptional responses to growth rate differences. Here we show that a similar mechanism-transitions from the HOC phase to the LOC phase-can account for much of the common environmental stress response (ESR) and for the cross-protection by a preliminary heat stress (or slow growth rate) to subsequent lethal heat stress. Similar to the budding yeast metabolic cycle, we suggest that a metabolic cycle, coupled in a similar way to the ESR, in the distantly related fission yeast, Schizosaccharomyces pombe, and in humans can explain gene expression and respiratory patterns observed in these eukaryotes. Although metabolic cycling is associated with the G0/G1 phase of the cell division cycle of slowly growing budding yeast, transcriptional cycling was detected in the G2 phase of the division cycle in fission yeast, consistent with the idea that respiratory metabolic cycling occurs during the phases of the cell division cycle associated with mass accumulation in these divergent eukaryotes., The respiratory metabolic cycle in budding yeast (Saccharomyces cerevisiae) consists of two phases that are most simply defined phenomenologically: low oxygen consumption (LOC) and high oxygen consumption (HOC). Each phase is associated with the periodic expression of thousands of genes, producing oscillating patterns of gene expression found in synchronized cultures and in single cells of slowly growing unsynchronized cultures. Systematic variation in the durations of the HOC and LOC phases can account quantitatively for well-studied transcriptional responses to growth rate differences. Here we show that a similar mechanism-transitions from the HOC phase to the LOC phase-can account for much of the common environmental stress response (ESR) and for the cross-protection by a preliminary heat stress (or slow growth rate) to subsequent lethal heat stress. Similar to the budding yeast metabolic cycle, we suggest that a metabolic cycle, coupled in a similar way to the ESR, in the distantly related fission yeast, Schizosaccharomyces pombe, and in humans can explain gene expression and respiratory patterns observed in these eukaryotes. Although metabolic cycling is associated with the G0/G1 phase of the cell division cycle of slowly growing budding yeast, transcriptional cycling was detected in the G2 phase of the division cycle in fission yeast, consistent with the idea that respiratory metabolic cycling occurs during the phases of the cell division cycle associated with mass accumulation in these divergent eukaryotes.

Published
2012

13. WISP genes are members of the connective tissue growth factor family that are up-regulated in Wnt-1-transformed cells and aberrantly expressed in human colon tumors\ud \ud

Author

Pennica, D., Swanson, T.A., Welsh, J.W., Roy, M.A., Lawrence, D.A., Lee, J., Brush, J., Taneyhill, L.A., Deuel, B., Lew, M., Watanabe, C., Cohen, R.L., Melhem, M.F., Finley, G.G., Quirke, P., Goddard, A.D., Hillan, K.J., Gurney, A.L., Botstein, D., and Levine, A.J.

Abstract

Wnt family members are critical to many developmental processes, and components of the Wnt signaling pathway have been linked to tumorigenesis in familial and sporadic colon carcinomas. Here we report the identification of two genes, WISP-1 and WISP-2, that are up-regulated in the mouse mammary epithelial cell line C57MG transformed by Wnt-1, but not by Wnt-4. Together with a third related gene, WISP-3, these proteins define a subfamily of the connective tissue growth factor family. Two distinct systems demonstrated WISP induction to be associated with the expression of Wnt-1. These included (i) C57MG cells infected with a Wnt-1 retroviral vector or expressing Wnt-1 under the control of a tetracyline repressible promoter, and (ii) Wnt-1 transgenic mice. The WISP-1 gene was localized to human chromosome 8q24.1-8q24.3. WISP-1 genomic DNA was amplified in colon cancer cell lines and in human colon tumors and its RNA overexpressed (2- to >30-fold) in 84% of the tumors examined compared with patient-matched normal mucosa. WISP-3 mapped to chromosome 6q22-6q23 and also was overexpressed (4- to >40-fold) in 63% of the colon tumors analyzed. In contrast, WISP-2 mapped to human chromosome 20q12-20q13 and its DNA was amplified, but RNA expression was reduced (2- to >30-fold) in 79% of the tumors. These results suggest that the WISP genes may be downstream of Wnt-1 signaling and that aberrant levels of WISP expression in colon cancer may play a role in colon tumorigenesis. \ud \ud

Published
1998

14. The nucleotide sequence of Saccharomyces cerevisiae chromosome XVI

Author

Bussey H, Rk, Storms, Ahmed A, Albermann K, Allen E, Ansorge W, Araujo R, Aparicio A, Barrell B, Badcock K, Vladimir Benes, Botstein D, Bowman S, Brückner M, Carpenter J, Jm, Cherry, Chung E, Churcher C, Coster F, Davis K, Rw, Davis, Fs, Dietrich, Delius H, DiPaolo T, and Hani J

Subjects
Fungal Proteins, Open Reading Frames, Base Sequence, Humans, Saccharomyces cerevisiae, Chromosomes, Fungal, DNA, Fungal
Abstract

The nucleotide sequence of the 948,061 base pairs of chromosome XVI has been determined, completing the sequence of the yeast genome. Chromosome XVI was the last yeast chromosome identified, and some of the genes mapped early to it, such as GAL4, PEP4 and RAD1 (ref. 2) have played important roles in the development of yeast biology. The architecture of this final chromosome seems to be typical of the large yeast chromosomes, and shows large duplications with other yeast chromosomes. Chromosome XVI contains 487 potential protein-encoding genes, 17 tRNA genes and two small nuclear RNA genes; 27% of the genes have significant similarities to human gene products, and 48% are new and of unknown biological function. Systematic efforts to explore gene function have begun.

Published
1997

15. The nucleotide sequence of Saccharomyces cerevisiae chromosome IV

Author

Jacq, C., Altmorbe, J., Andre, B., Arnold, W., Bahr, A., Ballesta, Jpg, Bargues, M., Baron, L., Becker, A., Biteau, N., Blocker, H., Blugeon, C., Boskovic, J., Brandt, P., Bruckner, M., Buitrago, Mj, Coster, F., Delaveau, T., Delrey, F., Dujon, B., Eide, Lg, Garciacantalejo, Jm, Goffeau, A., Gomezperis, A., Granotier, C., Hanemann, V., Hankeln, T., Hoheisel, Jd, Jager, W., Jimenez, A., Jonniaux, Jl, Kramer, C., Kuster, H., Laamanen, P., Legros, Y., Louis, E., Mollerrieker, S., Monnet, A., Moro, M., Mullerauer, S., Nussbaumer, B., Paricio, N., Paulin, L., Perea, J., Perezalonso, M., Perezortin, Je, Pohl, Tm, Prydz, H., Purnelle, B., Rasmussen, Sw, Remacha, M., Jose Luis Revuelta, Rieger, M., Salom, D., Saluz, Hp, Saiz, Je, Saren, Am, Schafer, M., Scharfe, M., Schmidt, Er, Schneider, C., Scholler, P., Schwarz, S., Solermira, A., Urrestarazu, La, Verhasselt, P., Vissers, S., Voet, M., Volckaert, G., Wagner, G., Wambutt, R., Wedler, E., Wedler, H., Wolfl, S., Harris, DE, Bowman, S., Brown, D., Churcher, Cm, Connor, R., Dedman, K., Gentles, S., Hamlin, N., Hunt, S., Jones, L., Mcdonald, S., Murphy, L., Niblett, D., Odell, C., Oliver, K., Rajandream, Ma, Richards, C., Shore, L., Walsh, Sv, Barrell, Bg, Dietrich, Fs, Mulligan, J., Allen, E., Araujo, R., Aviles, E., Berno, O., Carpenter, J., Chen, E., Cherry, Jm, Chung, E., Duncan, M., Hunickesmith, S., Hyman, R., Komp, C., Lashkari, D., Lew, H., Lin, D., Mosedale, D., Nakahara, K., Namath, A., Oefner, P., Oh, C., Petel, Fx, Roberts, D., Schramm, S., Schroeder, M., Shogren, T., Shroff, N., Winant, A., Yelton, M., Botstein, D., Davis, Rw, Johnston, M., Hillier, L., Riles, L., Albermann, K., Hani, J., Heumann, K., Kleine, K., Mewes, Hw, Zollner, A., and Zaccaria, P.

Subjects
Multidisciplinary, Base Sequence, Molecular Sequence Data, Saccharomyces cerevisiae, Chromosomes, Fungal, DNA, Fungal
Abstract

The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome IV has been determined. Apart from chromosome XII, which contains the 1-2 Mb rDNA cluster, chromosome IV is the longest S. cerevisiae chromosome. It was split into three parts, which were sequenced by a consortium from the European Community, the Sanger Centre, and groups from St Louis and Stanford in the United States. The sequence of 1,531,974 base pairs contains 796 predicted or known genes, 318 (39.9%) of which have been previously identified. Of the 478 new genes, 225 (28.3%) are homologous to previously identified genes and 253 (32%) have unknown functions or correspond to spurious open reading frames (ORFs). On average there is one gene approximately every two kilobases. Superimposed on alternating regional variations in G+C composition, there is a large central domain with a lower G+C content that contains all the yeast transposon (Ty) elements and most of the tRNA genes. Chromosome IV shares with chromosomes II, V, XII, XIII and XV some long clustered duplications which partly explain its origin.

Published
1997

16. A locus for Fanconi anemia on 16q determined by homozygosity mapping

Author

Gschwend, M., Levran, O., Kruglyak, L., Ranade, K., Verlander, P. C., Shen, S., Faure, S., Weissenbach, J., Altay, C., Lander, E. S., Arleen Auerbach, and Botstein, D.

Subjects
Genetic Markers, Genotype, Genome, Human, Homozygote, Chromosome Mapping, Pedigree, Consanguinity, Fanconi Anemia, Gene Frequency, Humans, Genetic Testing, Lod Score, Chromosomes, Human, Pair 16, Research Article
Abstract

We report the results of a genomewide scan using homozygosity mapping to identify genes causing Fanconi anemia, a genetically heterogeneous recessive disorder. By studying 23 inbred families, we detected linkage to a locus causing Fanconi anemia near marker D16S520 (16q24.3). Although -65% of our families displayed clear linkage to D16S520, we found strong evidence (P = .0013) of genetic heterogeneity. This result independently confirms the recent mapping of the FAA gene to chromosome 16 by Pronk et al. Family ascertainment was biased against a previously identified FAC gene on chromosome 9, and no linkage was observed to this locus. Simultaneous search analysis suggested several additional chromosomal regions that could account for a small fraction of Fanconi anemia in our families, but the sample size is insufficient to provide statistical significance. We also demonstrate the strong effect of marker allele frequencies on LOD scores obtained in homozygosity mapping and discuss ways to avoid false positives arising from this effect.

Published
1996

18. Saccharomyces Genome Database provides mutant phenotype data

Author

Engel, S. R., primary, Balakrishnan, R., additional, Binkley, G., additional, Christie, K. R., additional, Costanzo, M. C., additional, Dwight, S. S., additional, Fisk, D. G., additional, Hirschman, J. E., additional, Hitz, B. C., additional, Hong, E. L., additional, Krieger, C. J., additional, Livstone, M. S., additional, Miyasato, S. R., additional, Nash, R., additional, Oughtred, R., additional, Park, J., additional, Skrzypek, M. S., additional, Weng, S., additional, Wong, E. D., additional, Dolinski, K., additional, Botstein, D., additional, and Cherry, J. M., additional

Published
2009
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19. Gene Ontology annotations at SGD: new data sources and annotation methods

Author

Hong, E. L., primary, Balakrishnan, R., additional, Dong, Q., additional, Christie, K. R., additional, Park, J., additional, Binkley, G., additional, Costanzo, M. C., additional, Dwight, S. S., additional, Engel, S. R., additional, Fisk, D. G., additional, Hirschman, J. E., additional, Hitz, B. C., additional, Krieger, C. J., additional, Livstone, M. S., additional, Miyasato, S. R., additional, Nash, R. S., additional, Oughtred, R., additional, Skrzypek, M. S., additional, Weng, S., additional, Wong, E. D., additional, Zhu, K. K., additional, Dolinski, K., additional, Botstein, D., additional, and Cherry, J. M., additional

Published
2007
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20. The Saccharomyces Genome Database provides comprehensive information about the biology of S. cerevisiae and tools for studies in comparative genomics

Author

Hirschman, Jodi Ellen, primary, Engel, S., additional, Hong, E., additional, Balakrishnan, R., additional, Christie, K., additional, Costanzo, M., additional, Dwight, S., additional, Fisk, D., additional, Nash, R., additional, Park, J., additional, Skrzypek, M., additional, Dolinski, K., additional, Livstone, M., additional, Oughtred, R., additional, Andrada, R., additional, Binkley, G., additional, Dong, Q., additional, Hitz, B., additional, Miyasoto, S., additional, Schroeder, M., additional, Weng, S., additional, Wong, E., additional, Botstein, D., additional, and Cherry, J. M., additional

Published
2007
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21. Expanded protein information at SGD: new pages and proteome browser

Author

Nash, R., primary, Weng, S., additional, Hitz, B., additional, Balakrishnan, R., additional, Christie, K. R., additional, Costanzo, M. C., additional, Dwight, S. S., additional, Engel, S. R., additional, Fisk, D. G., additional, Hirschman, J. E., additional, Hong, E. L., additional, Livstone, M. S., additional, Oughtred, R., additional, Park, J., additional, Skrzypek, M., additional, Theesfeld, C. L., additional, Binkley, G., additional, Dong, Q., additional, Lane, C., additional, Miyasato, S., additional, Sethuraman, A., additional, Schroeder, M., additional, Dolinski, K., additional, Botstein, D., additional, and Cherry, J. M., additional

Published
2007
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30. A cDNA microarray gene expression database for cancer drug discovery

Author

Weinstein, J.N., primary, Scherf, U., additional, Ross, D., additional, Waltham, M., additional, Reinhold, R., additional, Zhou, Y., additional, Scudiero, D.A., additional, Smith, L.H., additional, Lee, J.K., additional, Shalon, D., additional, Lashkari, D., additional, Eisen, M., additional, Myers, T.M., additional, Sausville, E.A., additional, Botstein, D., additional, and Brown, P.O., additional

Published
1999
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31. The Lymphochip: A Specialized cDNA Microarray for the Genomic-scale Analysis of Gene Expression in Normal and Malignant Lymphocytes

Author

ALIZADEH, A., primary, EISEN, M., additional, DAVIS, R.E., additional, MA, C., additional, SABET, H., additional, TRAN, T., additional, POWELL, J. I., additional, YANG, L., additional, MARTI, G.E., additional, MOORE, D. T., additional, HUDSON, J.R., additional, CHAN, W.C., additional, GREINER, T., additional, WEISENBURGER, D., additional, ARMITAGE, J.O., additional, LOSSOS, I., additional, LEVY, R., additional, BOTSTEIN, D., additional, BROWN, P.O., additional, and STAUDT, L.M., additional

Published
1999
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32. Using the Saccharomyces Genome Database (SGD) for analysis of protein similarities and structure

Author

Chervitz, S. A., primary, Hester, E. T., additional, Ball, C. A., additional, Dolinski, K., additional, Dwight, S. S., additional, Harris, M. A., additional, Juvik, G., additional, Malekian, A., additional, Roberts, S., additional, Roe, T., additional, Scafe, C., additional, Schroeder, M., additional, Sherlock, G., additional, Weng, S., additional, Zhu, Y., additional, Cherry, J. M., additional, and Botstein, D., additional

Published
1999
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37. Evidence for linkage of bipolar disorder to HC 18 with a parent-of-origin effect

Author

Stine, O.C., primary, Xu, J., additional, Koskela, R., additional, McMahon, F.J., additional, Gschwend, M., additional, Friddle, C., additional, Clark, C., additional, McInnis, M.G., additional, Simpson, S.G., additional, Breschel, T., additional, Vishio, E., additional, Riskin, K., additional, Feilotter, H., additional, Chen, E., additional, Shen, S., additional, Folstein, S., additional, Meyers, D.A., additional, Botstein, D., additional, Marr, T.G., additional, and DePaulo, J.R., additional

Published
1996
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38. Update from the DANA consortium on the genetics of bipolar disorder

Author

Mclnnis, M. G., primary, Xu, J. F., additional, Simpson, S. G., additional, McMahon, F. J., additional, Friddle, C., additional, Stine, O. C., additional, Koskella, R. J., additional, MacKinnon, D. F., additional, Gschwend, M., additional, Meyers, D. A., additional, Botstein, D., additional, Marr, T. G., additional, and DePaulo, J. R., additional

Published
1996
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