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
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TLDR
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.Abstract:
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 to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.read more
Citations
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The BioPAX community standard for pathway data sharing
Emek Demir,Emek Demir,Michael P. Cary,Suzanne M. Paley,Ken Fukuda,Christian Lemer,Imre Vastrik,Guanming Wu,Peter D'Eustachio,Carl F. Schaefer,Joanne S. Luciano,Frank Schacherer,Irma Martínez-Flores,Zhenjun Hu,Verónica Jiménez-Jacinto,Geeta Joshi-Tope,Kumaran Kandasamy,Alejandra López-Fuentes,Huaiyu Mi,Elgar Pichler,Igor Rodchenkov,Andrea Splendiani,Andrea Splendiani,Sasha Tkachev,Jeremy Zucker,Gopal R. Gopinath,Harsha Rajasimha,Harsha Rajasimha,Ranjani Ramakrishnan,Imran Shah,Mustafa H Syed,Nadia Anwar,Özgün Babur,Özgün Babur,Michael L. Blinov,Erik Brauner,Dan Corwin,Sylva L. Donaldson,Frank Gibbons,Robert N. Goldberg,Peter Hornbeck,Augustin Luna,Peter Murray-Rust,Eric K. Neumann,Oliver Reubenacker,Matthias Samwald,Matthias Samwald,Martijn P. van Iersel,Sarala M. Wimalaratne,Keith Allen,Burk Braun,Michelle Whirl-Carrillo,Kei-Hoi Cheung,Kam D. Dahlquist,Andrew Finney,Marc Gillespie,Elizabeth M. Glass,Li Gong,Robin Haw,Michael Honig,Olivier Hubaut,David W. Kane,Shiva Krupa,Martina Kutmon,Julie Leonard,Debbie Marks,David Merberg,Victoria Petri,Alexander R. Pico,Dean Ravenscroft,Liya Ren,Nigam H. Shah,Margot Sunshine,Rebecca Tang,Ryan Whaley,Stan Letovksy,Kenneth H. Buetow,Andrey Rzhetsky,Vincent Schächter,Bruno S. Sobral,Ugur Dogrusoz,Shannon K. McWeeney,Mirit I. Aladjem,Ewan Birney,Julio Collado-Vides,Susumu Goto,Michael Hucka,Nicolas Le Novère,Natalia Maltsev,Akhilesh Pandey,Paul Thomas,Edgar Wingender,Peter D. Karp,Chris Sander,Gary D. Bader +94 more
TL;DR: Thousands of interactions, organized into thousands of pathways, from many organisms are available from a growing number of databases, and this large amount of pathway data in a computable form will support visualization, analysis and biological discovery.
Journal ArticleDOI
Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems
TL;DR: A simple extension of a sparse PLS exploratory approach is proposed to perform variable selection in a multiclass classification framework and has a classification performance similar to other wrapper or sparse discriminant analysis approaches on public microarray and SNP data sets.
Journal ArticleDOI
Large-scale whole-genome sequencing of the Icelandic population
Daniel F. Gudbjartsson,Hannes Helgason,Sigurjon A. Gudjonsson,Florian Zink,Asmundur Oddson,Arnaldur Gylfason,Søren Besenbacher,Gisli Magnusson,Bjarni V. Halldorsson,Eirikur Hjartarson,Gunnar Th. Sigurdsson,Simon N. Stacey,Michael L. Frigge,Hilma Holm,Jona Saemundsdottir,Hafdis T. Helgadottir,Hrefna Johannsdottir,Gunnlaugur Sigfússon,Gudmundur Thorgeirsson,Jon Th. Sverrisson,Solveig Gretarsdottir,G. Bragi Walters,Thorunn Rafnar,Bjarni Thjodleifsson,Einar Björnsson,Sigurdur Olafsson,Hildur Thorarinsdottir,Thora Steingrimsdottir,Thora S. Gudmundsdottir,Ásgeir Theodórs,Jon G. Jonasson,Asgeir Sigurdsson,Gyda Bjornsdottir,Jon J. Jonsson,Ólafur Thorarensen,Petur Ludvigsson,Hakon Gudbjartsson,Gudmundur I. Eyjolfsson,Olof Sigurdardottir,Isleifur Olafsson,David O. Arnar,Olafur Th Magnusson,Augustine Kong,Gisli Masson,Unnur Thorsteinsdottir,Agnar Helgason,Patrick Sulem,Kari Stefansson +47 more
TL;DR: The insights gained from sequencing the whole genomes of Icelanders to a median depth of 20× provide a study design that can be used to determine how variation in the sequence of the human genome gives rise to human diversity.
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Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development.
Michael F. Covington,Michael F. Covington,Julin N. Maloof,Marty Straume,Steve A. Kay,Steve A. Kay,Stacey L. Harmer +6 more
TL;DR: It is suggested that transcript abundance of roughly one-third of expressed A. thaliana genes is circadian regulated, suggesting that how the circadian clock affects plant growth and leads to improved fitness is understood.
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Plant-mPLoc: A Top-Down Strategy to Augment the Power for Predicting Plant Protein Subcellular Localization
Kuo-Chen Chou,Hong-Bin Shen +1 more
TL;DR: A new predictor called “Plant-mPLoc” is developed by integrating the gene ontology information, functional domain information, and sequential evolutionary information through three different modes of pseudo amino acid composition that has the capacity to deal with multiple-location proteins beyond the reach of any existing predictors specialized for identifying plant protein subcellular localization.
References
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TL;DR: The nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome is determined using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map.
Journal ArticleDOI
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
TL;DR: 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.
Journal ArticleDOI
Life with 6000 Genes
André Goffeau,Bart Barrell,Howard Bussey,Ronald W. Davis,Bernard Dujon,Horst Feldmann,Francis Galibert,J D Hoheisel,Claude Jacq,Mark Johnston,Edward J. Louis,Hans-Werner Mewes,Yasufumi Murakami,Peter Philippsen,Hervé Tettelin,Stephen G. Oliver +15 more
TL;DR: The genome of the yeast Saccharomyces cerevisiae has been completely sequenced through a worldwide collaboration and provides information about the higher order organization of yeast's 16 chromosomes and allows some insight into their evolutionary history.
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