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
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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Supporting data for "Draft genome of the leopard gecko, Eublepharis macularius"
Zijun Xiong,Fang Li,Qiye Li,Long Zhou,Tony Gamble,Jiao Zheng,Ling Kui,Cai Li,Shengbin Li,Huanming Yang,Guojie Zhang +10 more
TL;DR: Assembly of the leopard gecko genome provides a valuable resource for future comparative genomic studies of geckos and other squamate reptiles.
Journal ArticleDOI
Predicting synthetic lethal interactions using conserved patterns in protein interaction networks.
Graeme Benstead-Hume,Xiangrong Chen,Suzanna R. Hopkins,Karen A. Lane,Jessica A. Downs,Frances M. G. Pearl +5 more
TL;DR: SLant (Synthetic Lethal analysis via Network topology), a computational systems approach to predicting human synthetic lethal interactions that works by identifying and exploiting conserved patterns in protein interaction network topology both within and across species is described.
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Transcript levels of keratin 1/5/6/14/15/16/17 as potential prognostic indicators in melanoma patients.
TL;DR: In this article, the authors examined the transcriptional and clinical data of Keratins in patients with melanoma from GEO, TCGA, ONCOMINE, GEPIA, cBioPortal, TIMER and TISIDB databases and found that the mRNA levels of KRT1/2/5/6/8/10/14/15/16/17 were significantly differential expressed between primary melanoma and metastatic melanoma.
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From biological databases to platforms for biomedical discovery.
TL;DR: The use of different database systems to store biological information is discussed and some of the key emerging computing technologies are mentioned that are likely to have a key role in the future of bioinformatics are mentioned.
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Synergistic Genetic Interactions between Pkhd1 and Pkd1 Result in an ARPKD-Like Phenotype in Murine Models.
Rory J. Olson,Katharina Hopp,Harrison H. Wells,Jessica M. Smith,Jessica Furtado,Jessica Furtado,Megan M. Constans,Diana L. Escobar,Aron M. Geurts,Vicente E. Torres,Peter C. Harris +10 more
TL;DR: Data indicate that FPC and the polycystins work independently, with separate disease-causing thresholds; however, a combined protein threshold triggers the synergistic, cystogenic response because of enhanced dysregulation of primary cilia.
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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