Fields: Molecular Biology, Genetics & Genealogy, Biochemistry 
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Budding Yeast Cdna Microarray Cell Cycle Cell Line Dna Microarray Expression Pattern Gene Expression Pattern Gene Expression Profile Gene Expression Genetics Large Scale Saccharomyces Genome Database Transcription Factor Wild Type saccharomyces cerevisiae
被引用100次以上的学术论文如下：
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A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression.The output is displayed graphically, conveying the clustering and the underlying expression data simultaneously in a form intuitive for biologists. We have found in the budding yeast Saccharomyces ...Journal: Proceedings of The National Academy of Sciences - PNAS , vol. 95, no. 25, pp. 14863-14868, 1998
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Michael Ashburner, Catherine A. Ball, Judith A. Blake, , A P Davis, J T Eppig, M A Harris, D P Hill, J E Richardson, M RingwaldPublished in 2000.
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Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling (Citations: 2641)
Ash A. Alizadeh, Michael B. Eisen, R. Eric Davis, Izidore S. Lossos, Andreas Rosenwald, Jennifer C. Boldrick, Hajeer Sabet, Truc Tran, Xin Yu, John I. Powell, Liming Yang, Gerald E. Martihttp://academic.research.microsoft.com/io.ashx?type=5&id=1250903&selfId1=2239044&selfId2=-1&maxNumber=12&query=12 Pathology and Microbiology, and 13 Diffuse large B-cell lymphoma (DLBCL), the most common subtype of non-Hodgkin's lymphoma, is clinically heterogeneous: 40% of patients respond well to current therapy and have prolonged survival, whereas the remainder succumb to the disease. We proposed that this variability in natural history reflects unrecognized molecular heterogeneity in the tumours. Using DNA ... -
Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization (Citations: 2358) Paul Spellman, Gavin Sherlock, M. Zhang, Vishwanath R. Iyer, Kirk Anders, Michael B. Eisen, Patrick O. Brown, , Bruce FutcherWe sought to create a comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle. To this end, we used DNA microarrays and samples from yeast cultures synchronized by three independent methods: alpha factor arrest, elutriation, and arrest of a cdc15 temperature-sensitive mutant. Using periodicity and correlation algorithms, we identified 800 genes that meet an ...
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Charles M. Perou, Therese Sorlie, Michael B. Eisen, Matt van de Rijn, Stefanie S. Jeffrey, Christian A. Rees, Jonathan R. Pollack, Douglas T. Ross, Hilde Johnsen, Lars A. Aksien, Oystein Fluge, Alexander Pergamenschikovhttp://academic.research.microsoft.com/io.ashx?type=5&id=2031893&selfId1=2239044&selfId2=-1&maxNumber=12&query=
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Published in 1989.
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Therese Sørlie, Charles M. Perou, Robert Tibshirani, Turid Aas, Stephanie Geisler, Hilde Johnsen, Trevor Hastie, Michael B. Eisen, Matt van de Rijn, Stefanie S. Jeffrey, Thor Thorsen, Hanne Quisthttp://academic.research.microsoft.com/io.ashx?type=5&id=2038607&selfId1=2239044&selfId2=-1&maxNumber=12&query=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 out- come. 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 ...
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Audrey P. Gasch, Paul Spellman, Camilla M. Kao, Orna Carmel-harel, Michael B. Eisen, Gisela Storz, , Patrick O. BrownWe explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over time for almost every yeast gene, as cells responded to temperature shocks, hydrogen peroxide, the superoxide-generating drug menadione, the sulfhydryl-oxidizing agent diamide, the disulfide-reducing agent dithiothreitol, hyper- and hypo-osmotic shock, ...Published in 2000.
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Published in 1980.
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Thousands of genes are being discovered for the first time by sequencing the genomes of model organisms, an exhilarating reminder that much of the natural world remains to be explored at the molecular level. DNA microarrays provide a natural vehicle for this exploration. The model organisms are the first for which comprehensive genome-wide surveys of gene expression patterns or ...Published in 1999.
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Douglas T. Ross, Uwe Scherf, Michael B. Eisen, Charles M. Perou, Christian Rees, Paul Spellman, Vishwanath Iyer, Stefanie S. Jeffrey, Matt Van de Rijn, Mark Waltham, Alexander Pergamenschikov, Jeffrey C. F. Leehttp://academic.research.microsoft.com/io.ashx?type=5&id=1970139&selfId1=2239044&selfId2=-1&maxNumber=12&query=We used cDNA micro arrays to explore the variation in expression of approximately 8,000 unique genes among the 60 cell lines used in the National Cancer Institute s screen for anti-cancer drugs. Classification of the cell lines based solely on the observed patterns of gene expression revealed a correspondence to the ostensible origins of the tumors from which ...Published in 2000.
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Olga G. Troyanskaya, Michael Cantor, Gavin Sherlock, Patrick O. Brown, Trevor Hastie, Robert Tibshirani, , Russ B. AltmanMotivation: Gene expression microarray experiments can generate data sets with multiple missing expression val- ues. Unfortunately, many algorithms for gene expression analysis require a complete matrix of gene array values as input. For example, methods such as hierarchical cluster- ing and K-means clustering are not robust to missing data, and may lose effectiveness even with a few missing values. ...Journal: Bioinformatics/computer Applications in The Biosciences - BIOINFORMATICS , vol. 17, no. 6, pp. 520-525, 2001
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Singular value decomposition for genome-wide expression data processing and modeling (Citations: 720) We describe the use of singular value decomposition in transforming genome-wide expression data from genes × arrays space to reduced diagonalized "eigengenes" × "eigenarrays" space, where the eigengenes (or eigenarrays) are unique orthonormal superpositions of the genes (or arrays). Normalizing the data by filtering out the eigengenes (and eigenarrays) that are inferred to represent noise or experimental artifacts enables ...Journal: Proceedings of The National Academy of Sciences - PNAS , vol. 971, no. 18, pp. 10101-10106, 2000
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Much of a cell's activity is organized as a network of interacting modules: sets of genes coregulated to respond to different conditions. We present a probabilistic method for identifying regulatory modules from gene expression data. Our procedure identifies modules of coregulated genes, their regulators and the conditions under which regulation occurs, generating testable hypotheses in the form 'regulator X ...
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Jonathan R. Pollack, Charles M. Perou, Ash A. Alizadeh, Michael B. Eisen, Alexander Pergamenschikov, Cheryl F. Williams, Stefanie S. Jeffrey, , Patrick O. BrownGene amplifications and deletions frequently contribute to tumorigenesis. Characterization of these DNA copy-number changes is important for both the basic understanding of cancer and its diagnosis. Comparative genomic hybridization (CGH) was developed to survey DNA copy-number variations across a whole genome. With CGH, differentially labelled test and reference genomic DNAs are co-hybridized to normal metaphase chromosomes, and ...
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Distinctive Gene Expression Patterns in Human Mammary Epithelial Cells and Breast Cancers (Citations: 595) Charles M. Perou, Stefanie S. Jeffrey, Matt van de Rijn, Christian A. Rees, Michael B. Eisen, Douglas T. Ross, Alexander Pergamenschikov, Cheryl F. Williams, Shirley X. Zhu, Jeffrey C. F. Lee, Deval Lashkari, Dari Shalonhttp://academic.research.microsoft.com/io.ashx?type=5&id=1970137&selfId1=2239044&selfId2=-1&maxNumber=12&query=cDNA microarrays and a clustering algorithm were used to identify patterns of gene expression in human mammary epithelial cells growing in culture and in primary human breast tumors. Clusters of coexpressed genes identified through manipulations of mammary epithelial cells in vitro also showed consistent patterns of variation in expression among breast tumor samples. By using immunohistochemistry with antibodies against proteins ...Journal: Proceedings of The National Academy of Sciences - PNAS , vol. 96, no. 16, pp. 9212-9217, 1999
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Uwe Scherf, Douglas T. Ross, Mark Waltham, Lawrence H. Smith, Jae K. Lee, Lorraine Tanabe, Kurt W. Kohn, William C. Reinhold, Timothy G. Myers, Darren T. Andrews, Dominic A. Scudiero, Michael B. Eisenhttp://academic.research.microsoft.com/io.ashx?type=5&id=2083109&selfId1=2239044&selfId2=-1&maxNumber=12&query=We used cDNA microarrays to assess gene expression profiles in 60 human cancer cell lines used in a drug discov- ery screen by the National Cancer Institute. Using these data, we linked bioinformatics and chemoinformatics by correlating gene expression and drug activity patterns in the NCI60 lines. Clustering the cell lines on the basis of gene expression yielded relationships very ...Published in 2000.
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Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease (Citations: 552) The past two decades have witnessed an explosion in the identification, largely by positional cloning, of genes associated with mendelian diseases. The roughly 1,200 genes that have been characterized have clarified our understanding of the molecular basis of human genetic disease. The principles derived from these successes should be applied now to strategies aimed at finding the considerably more ...
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Mitchell E. Garber, Olga G. Troyanskaya, Karsten Schluens, Simone Petersen, Zsuzsanna Thaesler, Manuela Pacyna-Gengelbach, Matt van de Rijn, Glenn D. Rosen, Charles M. Perou, Richard I. Whyte, Russ B. Altman, Patrick O. Brownhttp://academic.research.microsoft.com/io.ashx?type=5&id=2978178&selfId1=2239044&selfId2=-1&maxNumber=12&query=Journal: Proceedings of The National Academy of Sciences - PNAS , vol. 981, no. 24, pp. 13784-13789, 2001
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Michael L. Whitfield, Gavin Sherlock, Alok J. Saldanha, John I. Murray, Catherine A. Ball, Karen E. Alexander, John C. Matese, Charles M. Perou, Myra M. Hurt, Patrick O. Brown,The genome-wide program of gene expression during the cell division cycle in a human cancer cell line (HeLa) was characterized using cDNA microarrays. Transcripts of 850 genes showed periodic variation during the cell cycle. Hierarchical clustering of the expression patterns revealed coexpressed groups of previously well-characterized genes involved in essential cell cycle pro- cesses such as DNA replication, ...
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Andreas Rosenwald, Ash A. Alizadeh, George Widhopf, Richard Simon, R. Eric Davis, Xin Yu, Liming Yang, Oxana K. Pickeral, Laura Z. Rassenti, John Powell, , John C. Byrdhttp://academic.research.microsoft.com/io.ashx?type=5&id=32892880&selfId1=2239044&selfId2=-1&maxNumber=12&query=The most common human leukemia is B cell chronic lymphocytic leukemia (CLL), a malig- nancy of mature B cells with a characteristic clinical presentation but a variable clinical course. The rearranged immunoglobulin (Ig) genes of CLL cells may be either germ-line in sequence or somatically mutated. Lack of Ig mutations defined a distinctly worse prognostic group of CLL patients ...
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V. R Iyer, M. B. Eisen, D. T. Ross, G. Schuler, T. Moore, J. C. F. Lee, M. Trent, L. M. Staudt, J. Hudson, M. S. Boguski, D. Lashkari, D. Shalonhttp://academic.research.microsoft.com/io.ashx?type=5&id=3973513&selfId1=2239044&selfId2=-1&maxNumber=12&query=
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J. Michael Cherry, Caroline Adler, Catherine A. Ball, Stephen A. Chervitz, Selina S. Dwight, Erich T. Hester, Yankai Jia, Gail Juvik, Taiyun Roe, Mark Schroeder, Shuai Weng,The Saccharomyces Genome Database (SGD) provides Internet access to the complete Saccharomyces cerevisiae genomic s equence, i ts g enes a nd t heir products, the p henotypes of i ts m utants, a nd t he literature supporting these data. The amount of information and t he n umber o f features p rovided b y SGD have i ...
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GO: : TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes (Citations: 343)
Journal: Bioinformatics/computer Applications in The Biosciences - BIOINFORMATICS , vol. 20, no. 18, pp. 3710-3715, 2004 -
An efficient strategy for mapping human genes that cause recessive traits has been devised that uses mapped restriction fragment length polymorphisms (RFLPs) and the DNA of affected children from consanguineous marriages. The method involves detection of the disease locus by virtue of the fact that the adjacent region will preferentially be homozygous by descent in such inbred children. A single ...
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Jacques Lapointe, Chunde Li, John P. Higgins, Matt van de Rijn, Eric Bair, Kelli Montgomery, Michelle Ferrari, Lars Egevad, Walter Rayford, Ulf Bergerheim, Peter Ekman, Angelo M. Demarzohttp://academic.research.microsoft.com/io.ashx?type=5&id=15170437&selfId1=2239044&selfId2=-1&maxNumber=12&query=Prostate cancer, a leading cause of cancer death, displays a broad range of clinical behavior from relatively indolent to aggressive metastatic disease. To explore potential molecular variation underlying this clinical heterogeneity, we profiled gene expression in 62 primary prostate tumors, as well as 41 normal prostate specimens and nine lymph node metastases, using cDNA microarrays containing 26,000 genes. Unsupervised ...Journal: Proceedings of The National Academy of Sciences - PNAS , vol. 101, no. 3, pp. 811-816, 2004
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Douglas T. Ross, Uwe Scherf, Michael B. Eisen, Charles M. Perou, Christian Rees, Paul Spellman, Vishwanath Iyer, Stefanie S. Jeffrey, Matt Van de Rijn, Mark Waltham, Alexander Pergamenschikov, Jeffrey C. F. Leehttp://academic.research.microsoft.com/io.ashx?type=5&id=37051739&selfId1=2239044&selfId2=-1&maxNumber=12&query=We used cDNA microarrays to explore the variation in expression of approximately 8,000 unique genes among the 60 cell lines used in the National Cancer Institute's screen for anti-cancer drugs. Classification of the cell lines based solely on the observed patterns of gene expression revealed a correspondence to the ostensible origins of the tumours from which the ...
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Laurie Issel-Tarver, Karen R. Christie, Kara Dolinski, Rey Andrada, Rama Balakrishnan, Catherine A. Ball, Gail Binkley, Stan Dong, Selina S. Dwight, Dianna G. Fisk, Midori Harris, Mark Schroederhttp://academic.research.microsoft.com/io.ashx?type=5&id=49031744&selfId1=2239044&selfId2=-1&maxNumber=12&query=
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Gavin Sherlock, Tina Hernandez-boussard, Andrew Kasarskis, Gail Binkley, John C. Matese, Selina S. Dwight, Miroslava Kaloper, Shuai Weng, Heng Jin, Catherine A. Ball, Michael B. Eisen, Paul T. Spellmanhttp://academic.research.microsoft.com/io.ashx?type=5&id=148897&selfId1=2239044&selfId2=-1&maxNumber=12&query=The Stanford Microarray Database (SMD) stores raw and normalized data from microarray experiments, and provides web interfaces for researchers to retrieve, analyze and visualize their data. The two immediate goals for SMD are to serve as a storage site for microarray data from ongoing research at Stanford University, and to facilitate the public dissemination of that data once published, or ...
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background Several gene-expression signatures can be used to predict the prognosis in diffuse large-B-cell lymphoma, but the lack of practical tests for a genome-scale analysis has restricted the use of this method. methods We studied 36 genes whose expression had been reported to predict survival in diffuse large-B-cell lymphoma. We measured the expression of ...
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Gene Expression Signature of Fibroblast Serum Response Predicts Human Cancer Progression: Similarities between Tumors and Wounds (Citations: 286) Howard Y. Chang, Julie B. Sneddon, Ash A. Alizadeh, Ruchira Sood, Rob B. West, Kelli Montgomery, Jen-Tsan Chi, Matt van de Rijn, , Patrick O. BrownCancer invasion and metastasis have been likened to wound healing gone awry. Despite parallels in cellular behavior between cancer progression and wound healing, the molecular relationships between these two processes and their prognostic implications are unclear. In this study, based on gene expression profiles of fibroblasts from ten anatomic sites, we identify a stereotyped gene expression program in response to ...
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We determined the distribution of repressor-activator protein 1 (Rap1) and the accessory silencing proteins Sir2, Sir3 and Sir4 in vivo on the entire yeast genome, at a resolution of 2 kb. Rap1 is central to the cellular economy during rapid growth, targeting 294 loci, about 5% of yeast genes, and participating in the activation of 37% of all RNA ...
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Xin Chen, Siu Tim Cheung, Samuel So, Sheung Tat Fan, Christopher Barry, John Higgins, Kin-Man Lai, Jiafu Ji, Sandrine Dudoit, Irene O. L. Ng, Matt van de Rijn, http://academic.research.microsoft.com/io.ashx?type=5&id=3137453&selfId1=2239044&selfId2=-1&maxNumber=12&query=Hepatocellular carcinoma (HCC) is a leading cause of death worldwide. Using cDNA microarrays to characterize patterns of gene expression in HCC, we found consistent differences between the expression patterns in HCC compared with those seen in nontumor liver tissues. The expression patterns in HCC were also readily distinguished from those associated with tumors metastatic to liver. The global gene expression ...
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Maximilian Diehn, Gavin Sherlock, Gail Binkley, Heng Jin, John C. Matese, Tina Hernandez-boussard, Christian A. Rees, J. Michael Cherry, , Patrick O. Brown, Ash A. AlizadehThe explosion in the number of functional genomic datasets generated with tools such as DNA micro- arrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that brings together information from a broad range of resources, and provides it in manner particularly useful for genome-scale analyses. ...
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Relation of Gene Expression Phenotype to Immunoglobulin Mutation Genotype in B Cell Chronic Lymphocytic Leukemia (Citations: 244) Andreas Rosenwald, Ash A. Alizadeh, George Widhopf, Richard Simon, R. Eric Davis, Xin Yu, Liming Yang, Oxana K. Pickeral, Laura Z. Rassenti, John Powell, , John C. Byrdhttp://academic.research.microsoft.com/io.ashx?type=5&id=4986643&selfId1=2239044&selfId2=-1&maxNumber=12&query=The most common human leukemia is B cell chronic lymphocytic leukemia (CLL), a malig- nancy of mature B cells with a characteristic clinical presentation but a variable clinical course. The rearranged immunoglobulin (Ig) genes of CLL cells may be either germ-line in sequence or somatically mutated. Lack of Ig mutations defined a distinctly worse prognostic group of CLL patients ...
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Trevor Hastie, Robert Tibshirani, Michael B. Eisen, Ash Alizadeh, Ronald Levy, Louis Staudt, Wing C. Chan, , Patrick BrownBACKGROUND: Large gene expression studies, such as those conducted using DNA arrays, often provide millions of different pieces of data. To address the problem of analyzing such data, we describe a statistical method, which we have called 'gene shaving'. The method identifies subsets of genes with coherent expression patterns and large variation across conditions. Gene shaving differs from hierarchical clustering ...
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Jeremy Gollub, Catherine A. Ball, Gail Binkley, Janos Demeter, David B. Finkelstein, Joan M. Hebert, Tina Hernandez-boussard, Heng Jin, Miroslava Kaloper, John C. Matese, Mark Schroeder, Patrick O. Brownhttp://academic.research.microsoft.com/io.ashx?type=5&id=749292&selfId1=2239044&selfId2=-1&maxNumber=12&query=The Stanford Microarray Database (SMD; http:// genome-www.stanford.edu/microarray/) serves as a microarray research database for Stanford investi- gators and their collaborators. In addition, SMD functions as a resource for the entire scientific community, by making freely available all of its source code and providing full public access to data published by SMD users, along with many tools ...
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Stephen A. Chervitz, L. Aravind, Gavin Sherlock, Catherine A. Ball, Eugene V. Koonin, Selina S. Dwight, Midori A. Harris, Kara Dolinski, Scott Mohr, Temple Smith, Shuai Weng, J. Michael Cherryhttp://academic.research.microsoft.com/io.ashx?type=5&id=2862069&selfId1=2239044&selfId2=-1&maxNumber=12&query=
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ABSTRACT Culturing a population of Saccharomyces cer- evisiae for many generations under conditions to which it is not optimally adapted selects for fitter genetic variants. This simple experimental design provides a tractable model of adaptive evolution under natural selection. Beginning with a clonal, founding population, independently evolved strains were obtained from three independent cultures after contin- uous aerobic growth in ...Journal: Proceedings of The National Academy of Sciences - PNAS , vol. 96, no. 17, pp. 9721-9726, 1999
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Helen Donis-Keller, Philip Green, Cynthia Helmes, Samuel Cartinhour, Barbara Weiffenbach, Karen Stephens, Tim P. Keith, Donald W. Bowden, Douglas R. Smith, Eric S. Lander, , Gita Akotshttp://academic.research.microsoft.com/io.ashx?type=5&id=11282196&selfId1=2239044&selfId2=-1&maxNumber=12&query=We report the construction of a linkage map of the human genome, based on the pattern of inheritance of 403 polymorphic loci, including 393 RFLPs, in a panel of DNAs from 21 three-generation families. By a combination of mathematical linkage analysis and physical localization of selected clones, it was possible to arrange these loci into linkage groups representing 23 ...
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Published in 2001.
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A fundamental feature of the architecture and functional design of vertebrate animals is a stroma, composed of extracellular matrix and mesenchymal cells, which provides a structural scaffold and conduit for blood and lymphatic vessels, nerves, and leukocytes. Reciprocal interactions between mesenchymal and epithelial cells are known to play a critical role in orchestrating the development and morphogenesis of tissues and ...Journal: Proceedings of The National Academy of Sciences - PNAS , vol. 991, no. 20, pp. 12877-12882, 2002
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A Bayesian framework for combining heterogeneous data sources for gene function prediction (in Saccharomyces cerevisiae) (Citations: 205) Journal: Proceedings of The National Academy of Sciences - PNAS , vol. 100, no. 14, pp. 8348-8353, 2003
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Jen-Tsan Chi, Howard Y. Chang, Guttorm Haraldsen, Frode L. Jahnsen, Olga G. Troyanskaya, Dustin S. Chang, Zhen Wang, Stanley G. Rockson, Matt van de Rijn, , Patrick O. BrownThe vascular system is locally specialized to accommodate widely varying blood flow and pressure and the distinct needs of individual tissues. The endothelial cells (ECs) that line the lumens of blood and lymphatic vessels play an integral role in the regional specialization of vascular structure and physiology. However, our understanding of EC diversity is limited. To explore EC specialization on ...Journal: Proceedings of The National Academy of Sciences - PNAS , vol. 1001, no. 19, pp. 10623-10628, 2003
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Jennifer C. Boldrick, Ash A. Alizadeh, Maximilian Diehn, Sandrine Dudoit, Chih Long Liu, Christopher E. Belcher, , Louis M. Staudt, Patrick O. Brown, David A. RelmanThe innate immune response is crucial for defense against microbial pathogens. To investigate the molecular choreography of this response, we carried out a systematic examination of the gene expression program in human peripheral blood mononuclear cells responding to bacteria and bacterial products. We found a remarkably stereotyped program of gene expression induced by bacterial lipopolysaccharide and diverse killed bacteria. An ...
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Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO) (Citations: 185) Selina S. Dwight, Midori A. Harris, Kara Dolinski, Catherine A. Ball, Gail Binkley, Karen R. Christie, Dianna G. Fisk, Laurie Issel-tarver, Mark Schroeder, Gavin Sherlock, Anand Sethuraman, Shuai Wenghttp://academic.research.microsoft.com/io.ashx?type=5&id=749644&selfId1=2239044&selfId2=-1&maxNumber=12&query=The Saccharomyces Genome Database (SGD) resources, ranging from genetic and physical maps to genome-wide analysis tools, reflect the scientific progress in identifying genes and their functions over the last decade. As emphasis shifts from identi- fication of the genes to identification of the role of their gene products in the cell, SGD seeks to provide its users with annotations ...
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J. Lapointe, C. Li, Van De Rijn, M Huggins, E. Bair, K. Montgomery, M. Ferrari, W. Rayford, P. Ekman, A. M. Demarzo, R. Tibshirani, http://academic.research.microsoft.com/io.ashx?type=5&id=3137462&selfId1=2239044&selfId2=-1&maxNumber=12&query=
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There are about 800 genes in Saccharomyces cerevisiae whose transcription is cell-cycle regulated. Some of these form clusters of co-regulated genes. The `CLB2' cluster contains 33 genes whose transcription peaks early in mitosis, including CLB1, CLB2, SWI5, ACE2, CDC5, CDC20 and other genes important for mitosis. Here we find that the genes in this cluster lose their cell ...
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Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms (Citations: 169) Karen R. Christie, Shuai Weng, Rama Balakrishnan, Maria C. Costanzo, Kara Dolinski, Selina S. Dwight, Stacia R. Engel, Becket Feierbach, Dianna G. Fisk, Jodi E. Hirschman, Eurie L. Hong, Laurie Issel-tarverhttp://academic.research.microsoft.com/io.ashx?type=5&id=1704233&selfId1=2239044&selfId2=-1&maxNumber=12&query=The Saccharomyces Genome Database (SGD; http:// www.yeastgenome.org/), a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, has recently developed several new resources that allow the comparison and integration of information on a genome-wide scale, enabling the user not only to find detailed information about individual genes, but also to make connections across ...
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Matt van de Rijn, Charles M. Perou, Rob Tibshirani, Phillippe Haas, Olli Kallioniemi, Juha Kononen, Joachim Torhorst, Guido Sauter, Markus Zuber, Ossi R. Köchli, Frank Mross, Holger Dieterichhttp://academic.research.microsoft.com/io.ashx?type=5&id=49011048&selfId1=2239044&selfId2=-1&maxNumber=12&query=
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Maximilian Diehn, Ash A. Alizadeh, Oliver J. Rando, Chih Long Liu, Kryn Stankunas, , Gerald R. Crabtree, Patrick O. BrownOptimal activation of T cells requires effective occupancy of both the antigen-specific T cell receptor and a second coreceptor such as CD28. We used cDNA microarrays to characterize the genomic expression program in human peripheral T cells responding to stimulation of these receptors. We found that CD28 agonists alone elicited few, but reproducible, changes in gene expression, whereas CD3 ...Journal: Proceedings of The National Academy of Sciences - PNAS , vol. 991, no. 18, pp. 11796-11801, 2002
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WISP Genes are Members of the Connective Tissue Growth Factor Family that are Up-Regulated in Wnt1-Transformed Cells and Aberrantly Expressed in Human Colon Tumors (Citations: 156) Diane Pennica, Todd A. Swanson, James W. Welsh, Margaret A. Roy, David A. Lawrence, James Lee, Jennifer Brush, Lisa A. Taneyhill, Bethanne Deuel, Michael Lew, Colin Watanabe, Robert L. Cohenhttp://academic.research.microsoft.com/io.ashx?type=5&id=11139619&selfId1=2239044&selfId2=-1&maxNumber=12&query=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-...Journal: Proceedings of The National Academy of Sciences - PNAS , vol. 951, no. 25, pp. 14717-14722, 1998
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Nonparametric methods for identifying differentially expressed genes in microarray data (Citations: 155) Motivation: Gene expression experiments provide a fast and systematic way to identify disease markers relevant to clinical care. In this study, we address the problem of robust identification of differentially expressed genes from microarray data. Differentially expressed genes, or discriminator genes, are genes with significantly different expression in two user-defined groups of microarray experiments. We compare three model-free ...Journal: Bioinformatics/computer Applications in The Biosciences - BIOINFORMATICS , vol. 18, no. 11, pp. 1454-1461, 2002
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Fusion proteins between the green fluorescent protein (GFP) and the cytoskeleton proteins Act1p (actin), Sac6p (yeast fimbrin homolog), and Abp1p in budding yeast (Saccharomyces cerevisiae) localize to the cortical actin patches. The actin fusions could not function as the sole actin source in yeast, but fusions between the actin-binding proteins Abp1p and Sac6p complement fully the phenotypes associated with ...Journal: Proceedings of The National Academy of Sciences - PNAS , vol. 93, no. 9, pp. 3886-3891, 1996
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Journal: Annals of The New York Academy of Sciences - ANN N Y ACAD SCI , vol. 354, no. 1 Genetic , pp. 484-491, 1980
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Genome rearrangements, especially amplifications and deletions, have regularly been observed as responses to sustained application of the same strong selective pressure in microbial populations growing in continuous culture. We studied eight strains of budding yeast (Saccharomyces cerevisiae) isolated after 100-500 generations of growth in glucose-limited chemostats. Changes in DNA copy number were assessed at single-gene resolution by ...
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Torsten O Nielsen, Rob B West, Sabine C Linn, Orly Alter, Margaret A Knowling, John X O'Connell, Shirley Zhu, Mike Fero, Gavin Sherlock, Jonathan R Pollack, Patrick O Brown, http://academic.research.microsoft.com/io.ashx?type=5&id=10212627&selfId1=2239044&selfId2=-1&maxNumber=12&query=Summary Background Soft-tissue tumours are derived from mesenchymal cells such as fibroblasts, muscle cells, or adipocytes, but for many such tumours the histogenesis is controversial. We aimed to start molecular characterisation of these rare neoplasms and to do a genome-wide search for new diagnostic markers. Methods We analysed gene-expression patterns of 41 soft- tissue tumours with spotted ...
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Jonathan R. Pollack, Charles M. Perou, Therese Sorlie, Ash A. Alizadeh, Christian Rees, Michael B. Eise, Alexander Pergamenschikov, Cheryl F. Williams, Matt van de Rijn, Stefanie S. Jeffrey, Hilde Johnsen, Per E. Lonninghttp://academic.research.microsoft.com/io.ashx?type=5&id=37051676&selfId1=2239044&selfId2=-1&maxNumber=12&query=
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Published in 1992.
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We have used in vitro mutagenesis and gene replacement to construct five new cold-sensitive muta- tions in TUB2, the sole gene encoding 13-tubulin in the yeast Saccharomyces cerevisiae. These and one previ- ously isolated tub2 mutant display diverse phenotypes that have allowed us to define the functions of yeast microtubules in vivo. At the restrictive temperature, all of ...Published in 1988.
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Teresa Reguly, Ashton Breitkreutz, Lorrie Boucher, Bobby-Joe Breitkreutz, Gary C Hon, Chad L Myers, Ainslie Parsons, Helena Friesen, Rose Oughtred, Amy Tong, Chris Stark, Yuen Hohttp://academic.research.microsoft.com/io.ashx?type=5&id=39207514&selfId1=2239044&selfId2=-1&maxNumber=12&query=ABSTRACT: BACKGROUND: The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet ...
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consistent within a factor of 2, with expectations based on estab- lished Trp protein levels. Several operons known to be regulated by the TyrR protein, aroF-tyrA, aroL, aroP, and aroG, were down-regu- lated on addition of tryptophan. TyrR can be activated by any one of the three aromatic amino acids. Only one operon, tnaAB, was signif- icantly activated ...Journal: Proceedings of The National Academy of Sciences - PNAS , vol. 97, no. 22, pp. 12170-12175, 2000
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Published in 1980.
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Koustubh Ranade, Chih-Tai Ting, Dee Pei, Chin-Fu Hsiao, Robert Pesich, Joan Hebert, Yii-Der I. Chen, Victor J. Dzau, David Curb, Richard Olshen, David R. Cox,Published in 2001.
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Utilization of sucrose as a source of carbon and energy in yeast (Sac- charomyces) is controlled by the classical SUC genes, which confer the ability to produce the sucrose-degrading enzyme invertase ( MORTIMER and HAW- THORNE 1969). Mutants of S. cereuisiae strain S288C (SuCZ+) unable to grow anaerobically on sucrose, but still able to use glucose, were isolated. Two major ...Published in 1981.
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Generalized singular value decomposition for comparative analysis of genome-scale expression data sets of two different organisms (Citations: 119) We describe a comparative mathematical framework for two genome-scale expression data sets. This framework formulates expression as superposition of the effects of regulatory programs, biological processes, and experimental artifacts common to both data sets, as well as those that are exclusive to one data set or the other, by using generalized singular value decomposition. This framework enables comparative reconstruction ...Journal: Proceedings of The National Academy of Sciences - PNAS , vol. 100, no. 6, pp. 3351-3356, 2003
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Yu Liang, Maximilian Diehn, Nathan Watson, Andrew W. Bollen, Ken D. Aldape, M. Kelly Nicholas, Kathleen R. Lamborn, Mitchel S. Berger, , Patrick O. Brown, Mark A. IsraelGlioblastoma multiforme (GBM) is the most common form of malignant glioma, characterized by genetic instability, intratumoral histopathological variability, and unpredictable clinical behavior. We investigated global gene expression in surgical samples of brain tumors. Gene expression profiling revealed large differences between normal brain samples and tumor tissues and between GBMs and lower-grade oligodendroglial tumors. Extensive differences in gene expression were ...Journal: Proceedings of The National Academy of Sciences - PNAS , vol. 102, no. 16, pp. 5814-5819, 2005
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A. ALIZADEH, M. EISEN, R. E. DAVIS, C. MA, H. SABET, T. TRAN, J. I. POWELL, L. YANG, G. E. MARTI, D. T. MOORE, J. R. HUDSON, W. C. CHANhttp://academic.research.microsoft.com/io.ashx?type=5&id=37798840&selfId1=2239044&selfId2=-1&maxNumber=12&query=Journal: Cold Spring Harbor Symposia on Quantitative Biology - COLD SPRING HARBOR SYMP , vol. 64, no. 1, pp. 71-78, 1999
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Three yeast actin-binding proteins were identified using yeast actin filaments as an affinity ma- trix. One protein appears to be a yeast myosin heavy chain; it is dissociated from actin filaments by ATP, it is similar in size (200 kD) to other myosins, and anti- bodies directed against Dictyostelium myosin heavy chain bind to it. Immunofluorescence experiments show that ...
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Marci E. Schaner, Douglas T. Ross, Giuseppe Ciaravino, Therese Sørlie, Olga Troyanskaya, Maximilian Diehn, Yan C. Wang, George E. Duran, Thomas L. Sikic, Sandra Caldeira, Hanne Skomedal, I-Ping Tuhttp://academic.research.microsoft.com/io.ashx?type=5&id=4987902&selfId1=2239044&selfId2=-1&maxNumber=12&query=We used DNA microarrays to characterize the global gene expression patterns in surface epithelial cancers of the ovary. We identified groups of genes that distinguished the clear cell subtype from other ovarian carcinomas, grade I and II from grade III serous papillary carcinomas, and ovarian from breast carcinomas. Six clear cell carcinomas were distinguished from 36 other ovarian carcinomas (predominantly ...
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Michael Ashburner, Catherine A. Ball, Judith A. Blake, , Heather Butler, J. Michael Cherry, Allan P. Davis, Kara Dolinski, Selina S. Dwight, Janan T. Eppig, Midori A. Harris, David P. Hillhttp://academic.research.microsoft.com/io.ashx?type=5&id=3901868&selfId1=2239044&selfId2=-1&maxNumber=12&query=Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied ...
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Summary A DNA fragment from yeast (Saccharomyces cere- visiae) was identified by its homology to a chicken p-tubulin cDNA and cloned. The fragment was shown to be unique in the yeast genome and to contain the gene for yeast fi-tubulin, since it can complement a benomyl-resistant conditional-lethal mutation. A smaller subfragment, when used to di- rect ...
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Different Gene Expression Patterns in Invasive Lobular and Ductal Carcinomas of the Breast (Citations: 109)
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Genetic footprinting was used to assess the phenotypic effects of Ty1 transposon insertions in 268 predicted genes of chromosome V of Saccharomyces cerevisiae. When seven selection protocols were used, Ty1 insertions in more than half the genes tested (157 of 268) were found to result in a detectable reduction in fitness. Results could not be obtained for fewer than 3 ...
Yeast cell cycle protein CDC48p shows full-length homology to the mammalian protein VCP and is a member of a protein family involved in secretion, peroxisome formation, and gene expression (Citations: 103)
Kai-Uwe Frohlich, Hans-Werner Fries, , Dieter Mecke
Yeast mutants of cell cycle gene cdc481 ar- rest as large budded cells with microtubules spreading aberrantly throughout the cytoplasm from a single spin- dle plaque . The gene was cloned and disruption proved it to be essential . The CDC48 sequence encodes a pro- tein of 92 kD that has an internal duplication of 200 amino acids and includes a nucleotide ...
Journal: Journal of Cell Biology - J CELL BIOL , vol. 114, no. 3, pp. 443-453, 1991
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