Comprehensive Identification of Cell Cycle–regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization
Paul T. Spellman,Gavin Sherlock,Gavin Sherlock,Michael Q. Zhang,Vishwanath R. Iyer,Kirk R. Anders,Michael B. Eisen,Patrick O. Brown,Patrick O. Brown,David Botstein,Bruce Futcher +10 more
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TLDR
A comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle is created, and it is found that the mRNA levels of more than half of these 800 genes respond to one or both of these cyclins.Abstract:
We 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 sync...read more
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Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
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Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.
Todd R. Golub,Todd R. Golub,Donna K. Slonim,Pablo Tamayo,Christine Huard,Michelle Gaasenbeek,Jill P. Mesirov,Hilary A. Coller,Mignon L. Loh,James R. Downing,Michael A. Caligiuri,Clara D. Bloomfield,Eric S. Lander +12 more
TL;DR: A generic approach to cancer classification based on gene expression monitoring by DNA microarrays is described and applied to human acute leukemias as a test case and suggests a general strategy for discovering and predicting cancer classes for other types of cancer, independent of previous biological knowledge.
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Survey of clustering algorithms
Rui Xu,Donald C. Wunsch +1 more
TL;DR: Clustering algorithms for data sets appearing in statistics, computer science, and machine learning are surveyed, and their applications in some benchmark data sets, the traveling salesman problem, and bioinformatics, a new field attracting intensive efforts are illustrated.
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The Perseus computational platform for comprehensive analysis of (prote)omics data.
Stefka Tyanova,Tikira Temu,Pavel Sinitcyn,Arthur Carlson,Marco Y. Hein,Tamar Geiger,Matthias Mann,Jürgen Cox +7 more
TL;DR: The Perseus software platform was developed to support biological and biomedical researchers in interpreting protein quantification, interaction and post-translational modification data and it is anticipated that Perseus's arsenal of algorithms and its intuitive usability will empower interdisciplinary analysis of complex large data sets.
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A General Framework for Weighted Gene Co-Expression Network Analysis
Bin Zhang,Steve Horvath +1 more
TL;DR: A general framework for `soft' thresholding that assigns a connection weight to each gene pair is described and several node connectivity measures are introduced and provided empirical evidence that they can be important for predicting the biological significance of a gene.
References
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Journal ArticleDOI
A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase
TL;DR: Strains deleted for both MBP1 and SWI4 were inviable, demonstrating that transcriptional activation by MBF and SBF has an important role in the transition from G1 to S phase.
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Mechanisms that help the yeast cell cycle clock tick: G2 cyclins transcriptionally activate G2 cyclins and repress G1 cyclins
TL;DR: It is found that the CLBs play a central role in the transition from CLNs to CLBs: theCLBs stimulate their own expression while repressing that of CLNs.
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Pds1p, an inhibitor of anaphase in budding yeast, plays a critical role in the APC and checkpoint pathway(s).
TL;DR: The isolation and characterization of pds1 mutants in Saccharomyces cerevisiae are reported and it is suggested that Pds1 protein is an anaphase inhibitor that plays a critical role in the control of anaphases by both APC and checkpoints.
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Asymmetric Accumulation of Ash1p in Postanaphase Nuclei Depends on a Myosin and Restricts Yeast Mating-Type Switching to Mother Cells
TL;DR: A gene is described, ASH1, that is necessary to repress HO in daughters and encodes a zinc finger protein whose preferential accumulation in daughter cell nuclei at the end of anaphase depends on She1p/Myo4p.
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Characterization of four B-type cyclin genes of the budding yeast Saccharomyces cerevisiae.
I. Fitch,Christian Dahmann,Uttam Surana,Angelika Amon,Kim Nasmyth,L Goetsch,B Byers,Bruce Futcher +7 more
TL;DR: The sequences of another related pair of B-type cyclin genes, which are term CLB3 and CLB4, are presented and it is suggested that the two groups of Clbs may have distinct roles in spindle formation and elongation.