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
Reads0
Chats0
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
More filters
Journal ArticleDOI
Impacts of bioinformatics to medicinal chemistry.
TL;DR: This minireview is to summarize the progresses by focusing on the following six aspects: Use the pseudo amino acid composition or PseAAC to predict various attributes of protein/peptide sequences that are useful for drug development.
Journal ArticleDOI
De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits
Yinghui Li,Guangyu Zhou,Jianxin Ma,Wenkai Jiang,Long-guo Jin,Zhouhao Zhang,Yong Guo,Jinbo Zhang,Yi Sui,Liangtao Zheng,Shan-shan Zhang,Qiyang Zuo,Shi Xuehui,Yanfei Li,Wan-ke Zhang,Yiyao Hu,Guanyi Kong,Huilong Hong,Bing Tan,Jian Song,Zhangxiong Liu,Yaoshen Wang,Hang Ruan,Carol K.L. Yeung,Jian Liu,Hailong Wang,Lijuan Zhang,Rongxia Guan,Kejing Wang,Wenbin Li,Shou-yi Chen,Ruzhen Chang,Zhi Jiang,Scott A. Jackson,Ruiqiang Li,Lijuan Qiu +35 more
TL;DR: Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass.
Journal ArticleDOI
Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps
TL;DR: A network-flow based algorithm, FunctionalFlow, is developed that exploits the underlying structure of protein interaction maps in order to predict protein function and has improved performance over previous methods in predicting the function of proteins with few (or no) annotated protein neighbors.
Journal ArticleDOI
Somatic mutation in single human neurons tracks developmental and transcriptional history.
Michael A. Lodato,Mollie B. Woodworth,Semin Lee,Gilad D. Evrony,Bhaven K. Mehta,Amir Karger,Soohyun Lee,Thomas Chittenden,Alissa M. D'Gama,Xuyu Cai,Lovelace J. Luquette,Eunjung Lee,Eunjung Lee,Peter J. Park,Peter J. Park,Christopher A. Walsh +15 more
TL;DR: Somatic mutations in the brain represent a durable and ongoing record of neuronal life history, from development through postmitotic function, and create nested lineage trees, allowing them to be dated relative to developmental landmarks and revealing a polyclonal architecture of the human cerebral cortex.
Journal ArticleDOI
Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death.
Michael A. Kohanski,Daniel J. Dwyer,Jamey Wierzbowski,Guillaume Cottarel,James J. Collins,James J. Collins +5 more
TL;DR: It is shown, by disabling systems that facilitate membrane protein traffic, that mistranslation and misfolding of membrane proteins are central to aminoglycoside-induced oxidative stress and cell death.
References
More filters
Journal ArticleDOI
Cluster analysis and display of genome-wide expression patterns
TL;DR: 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, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
Journal ArticleDOI
The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Journal ArticleDOI
The genome sequence of Drosophila melanogaster
Mark Raymond Adams,Susan E. Celniker,Robert A. Holt,Cheryl A. Evans,Jeannine D. Gocayne,Peter Amanatides,Steve Scherer,Peter W. Li,Roger A. Hoskins,R. Galle,Reed A. George,Suzanna E. Lewis,Stephen Richards,Michael Ashburner,Scott Henderson,Granger G. Sutton,Jennifer R. Wortman,Mark Yandell,Qing Zhang,Lin Chen,Rhonda C. Brandon,Yu-Hui Rogers,R. Blazej,Mark Champe,Barret D. Pfeiffer,Kenneth H. Wan,Colleen Doyle,E. G. Baxter,Gregg Helt,Catherine R. Nelson,G. L. Gabor Miklos,Josep F. Abril,A. Agbayani,Huijin An,C. Andrews-Pfannkoch,Danita Baldwin,Richard M. Ballew,Anand Basu,James Baxendale,Leyla Bayraktaroglu,Ellen M. Beasley,Karen Beeson,Panayiotis V. Benos,Benjamin P. Berman,D. Bhandari,Slava Bolshakov,Dana Borkova,Michael R. Botchan,John Bouck,Peter Brokstein,Philippe Brottier,Kenneth C. Burtis,Dana A. Busam,Heather Butler,Edouard Cadieu,I. Chandra,J. Michael Cherry,Simon Cawley,Carl Dahlke,Lionel Davenport,P. Davies,B. de Pablos,Arthur L. Delcher,Zuoming Deng,A. Deslattes Mays,Ian M. Dew,Susanne Dietz,Kristina Dodson,Lisa Doup,Michael Downes,Shannon Dugan-Rocha,B. C. Dunkov,Patrick J. Dunn,K. J. Durbin,Carlos Evangelista,Concepcion Ferraz,Steven Ferriera,Wolfgang Fleischmann,Carl Fosler,Andrei Gabrielian,Neha Garg,William M. Gelbart,Kenneth Glasser,A. Glodek,Fangcheng Gong,J. Harley Gorrell,Zhiping Gu,Ping Guan,Michael Harris,Nomi L. Harris,Damon A. Harvey,Thomas J. Heiman,Judith Hernandez,Jarrett Houck,Damon Hostin,K. Houston,Timothy Howland,Ming-Hui Wei,Chinyere Ibegwam,M. Jalali,Francis Kalush,Gary H. Karpen,Zhaoxi Ke,James A. Kennison,K. A. Ketchum,B. E. Kimmel,Chinnappa D. Kodira,Cheryl L. Kraft,Saul A. Kravitz,David Kulp,Zhongwu Lai,Paul Lasko,Yiding Lei,Alexander Levitsky,Jun Li,Zhenya Li,Yunye Liang,Xiaoying Lin,Xiangjun Liu,B. Mattei,Tina C. McIntosh,Michael P. McLeod,D. McPherson,Gennady V. Merkulov,Natalia Milshina,Clark M. Mobarry,J. Morris,A. Moshrefi,Stephen M. Mount,Mee Moy,Brian Murphy,Lee Murphy,Donna M. Muzny,David L. Nelson,David R. Nelson,Keith Nelson,K. Nixon,Deborah R. Nusskern,Joanne Pacleb,Michael J. Palazzolo,G. S. Pittman,Sue Pan,J. Pollard,Vinita Puri,Martin G. Reese,Knut Reinert,Karin A. Remington,Robert D. C. Saunders,Robert D. C. Saunders,F. Scheeler,H. Shen,B. Christopher Shue,Inga Siden-Kiamos,Michael Simpson,Marian P. Skupski,Thomas J. Smith,Eugene G. Spier,Allan C. Spradling,Mark Stapleton,Renee Strong,E. Sun,Robert Svirskas,C. Tector,Russell Turner,Eli Venter,Aihui Wang,Xianyuan Wang,Zhen Yuan Wang,David A. Wassarman,George M. Weinstock,Jean Weissenbach,Sherita Williams,Trevor Woodage,Kim C. Worley,D. Wu,Shih-Hung Yang,Q. Alison Yao,Jane Ye,R. F. Yeh,Jayshree Zaveri,Ming Zhan,Gefei Zhang,Qi Zhao,Liansheng Zheng,Xiangqun Zheng,Fei Zhong,Wenyan Zhong,X. Zhou,Shiaoping C. Zhu,Xiancan Zhu,Hamilton O. Smith,Richard A. Gibbs,Eugene W. Myers,Gerald M. Rubin,J. Craig Venter +194 more
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.
Related Papers (5)
Controlling the false discovery rate: a practical and powerful approach to multiple testing
Yoav Benjamini,Yosef Hochberg +1 more