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
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Improved detection of overrepresentation of Gene-Ontology annotations with parent–child analysis
TL;DR: A novel approach to analysis of GO term overrepresentation that determines over representation of terms in the context of annotations to the term's parents is presented, which reduces the dependencies between the individual term's measurements, and thereby avoids producing false-positive results owing to the inheritance problem.
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STITCH 4: integration of protein–chemical interactions with user data
Michael Kuhn,Damian Szklarczyk,Sune Pletscher-Frankild,Thomas Blicher,Christian von Mering,Lars Juhl Jensen,Peer Bork +6 more
TL;DR: This version of STITCH added features for users to upload their own data to STITCH in the form of internal identifiers, chemical structures or quantitative data, and changed the scheme for transferring interactions between species to rely on orthology rather than protein similarity.
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Quantifying the relationship between co-expression, co-regulation and gene function.
TL;DR: Data from a recent genome wide binding analysis is used in combination with mRNA expression data and existing functional annotations to quantify the likelihood that genes with varying degrees of similarity in mRNA expression profile or function will be bound by a common transcription factor.
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Molecular Signatures of Proliferation and Quiescence in Hematopoietic Stem Cells
Teresa A. Venezia,Akil Merchant,Akil Merchant,Carlos A. Ramos,Carlos A. Ramos,Nathan L. Whitehouse,Andrew S. Young,Chad A. Shaw,Margaret A. Goodell +8 more
TL;DR: The gene expression changes that occur over a time course when hematopoietic stem cells are induced to proliferate and return to quiescence in vivo are examined and a molecular model of the HSC activation cycle is built.
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Large-scale prediction of Saccharomyces cerevisiae gene function using overlapping transcriptional clusters
Lani F. Wu,Timothy P. Hughes,Armaity P. Davierwala,Mark D. Robinson,Roland Stoughton,Steven J. Altschuler +5 more
TL;DR: This work identifies potential new members of many existing functional categories including 285 candidate proteins involved in transcription, processing and transport of non-coding RNA molecules and presents experimental validation confirming the involvement of several of these proteins in ribosomal RNA processing.
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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