Literature DB >> 14681407

The Gene Ontology (GO) database and informatics resource.

M A Harris1, J Clark, A Ireland, J Lomax, M Ashburner, R Foulger, K Eilbeck, S Lewis, B Marshall, C Mungall, J Richter, G M Rubin, J A Blake, C Bult, M Dolan, H Drabkin, J T Eppig, D P Hill, L Ni, M Ringwald, R Balakrishnan, J M Cherry, K R Christie, M C Costanzo, S S Dwight, S Engel, D G Fisk, J E Hirschman, E L Hong, R S Nash, A Sethuraman, C L Theesfeld, D Botstein, K Dolinski, B Feierbach, T Berardini, S Mundodi, S Y Rhee, R Apweiler, D Barrell, E Camon, E Dimmer, V Lee, R Chisholm, P Gaudet, W Kibbe, R Kishore, E M Schwarz, P Sternberg, M Gwinn, L Hannick, J Wortman, M Berriman, V Wood, N de la Cruz, P Tonellato, P Jaiswal, T Seigfried, R White.   

Abstract

The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.

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Year:  2004        PMID: 14681407      PMCID: PMC308770          DOI: 10.1093/nar/gkh036

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  10 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

Review 2.  Ontology-based knowledge representation for bioinformatics.

Authors:  R Stevens; C A Goble; S Bechhofer
Journal:  Brief Bioinform       Date:  2000-11       Impact factor: 11.622

3.  Creating the gene ontology resource: design and implementation.

Authors: 
Journal:  Genome Res       Date:  2001-08       Impact factor: 9.043

4.  DIAN: a novel algorithm for genome ontological classification.

Authors:  Y Pouliot; J Gao; Q J Su; G G Liu; X B Ling
Journal:  Genome Res       Date:  2001-10       Impact factor: 9.043

5.  Large-scale protein annotation through gene ontology.

Authors:  Hanqing Xie; Alon Wasserman; Zurit Levine; Amit Novik; Vladimir Grebinskiy; Avi Shoshan; Liat Mintz
Journal:  Genome Res       Date:  2002-05       Impact factor: 9.043

6.  Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Authors:  Y Okazaki; M Furuno; T Kasukawa; J Adachi; H Bono; S Kondo; I Nikaido; N Osato; R Saito; H Suzuki; I Yamanaka; H Kiyosawa; K Yagi; Y Tomaru; Y Hasegawa; A Nogami; C Schönbach; T Gojobori; R Baldarelli; D P Hill; C Bult; D A Hume; J Quackenbush; L M Schriml; A Kanapin; H Matsuda; S Batalov; K W Beisel; J A Blake; D Bradt; V Brusic; C Chothia; L E Corbani; S Cousins; E Dalla; T A Dragani; C F Fletcher; A Forrest; K S Frazer; T Gaasterland; M Gariboldi; C Gissi; A Godzik; J Gough; S Grimmond; S Gustincich; N Hirokawa; I J Jackson; E D Jarvis; A Kanai; H Kawaji; Y Kawasawa; R M Kedzierski; B L King; A Konagaya; I V Kurochkin; Y Lee; B Lenhard; P A Lyons; D R Maglott; L Maltais; L Marchionni; L McKenzie; H Miki; T Nagashima; K Numata; T Okido; W J Pavan; G Pertea; G Pesole; N Petrovsky; R Pillai; J U Pontius; D Qi; S Ramachandran; T Ravasi; J C Reed; D J Reed; J Reid; B Z Ring; M Ringwald; A Sandelin; C Schneider; C A M Semple; M Setou; K Shimada; R Sultana; Y Takenaka; M S Taylor; R D Teasdale; M Tomita; R Verardo; L Wagner; C Wahlestedt; Y Wang; Y Watanabe; C Wells; L G Wilming; A Wynshaw-Boris; M Yanagisawa; I Yang; L Yang; Z Yuan; M Zavolan; Y Zhu; A Zimmer; P Carninci; N Hayatsu; T Hirozane-Kishikawa; H Konno; M Nakamura; N Sakazume; K Sato; T Shiraki; K Waki; J Kawai; K Aizawa; T Arakawa; S Fukuda; A Hara; W Hashizume; K Imotani; Y Ishii; M Itoh; I Kagawa; A Miyazaki; K Sakai; D Sasaki; K Shibata; A Shinagawa; A Yasunishi; M Yoshino; R Waterston; E S Lander; J Rogers; E Birney; Y Hayashizaki
Journal:  Nature       Date:  2002-12-05       Impact factor: 49.962

7.  The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.

Authors:  Evelyn Camon; Michele Magrane; Daniel Barrell; David Binns; Wolfgang Fleischmann; Paul Kersey; Nicola Mulder; Tom Oinn; John Maslen; Anthony Cox; Rolf Apweiler
Journal:  Genome Res       Date:  2003-03-12       Impact factor: 9.043

8.  Assessment of genome-wide protein function classification for Drosophila melanogaster.

Authors:  Huaiyu Mi; Jody Vandergriff; Michael Campbell; Apurva Narechania; William Majoros; Suzanna Lewis; Paul D Thomas; Michael Ashburner
Journal:  Genome Res       Date:  2003-09       Impact factor: 9.043

9.  Ontologies for molecular biology.

Authors:  S Schulze-Kremer
Journal:  Pac Symp Biocomput       Date:  1998

10.  The genome sequence of Drosophila melanogaster.

Authors:  M D Adams; S E Celniker; R A Holt; C A Evans; J D Gocayne; P G Amanatides; S E Scherer; P W Li; R A Hoskins; R F Galle; R A George; S E Lewis; S Richards; M Ashburner; S N Henderson; G G Sutton; J R Wortman; M D Yandell; Q Zhang; L X Chen; R C Brandon; Y H Rogers; R G Blazej; M Champe; B D Pfeiffer; K H Wan; C Doyle; E G Baxter; G Helt; C R Nelson; G L Gabor; J F Abril; A Agbayani; H J An; C Andrews-Pfannkoch; D Baldwin; R M Ballew; A Basu; J Baxendale; L Bayraktaroglu; E M Beasley; K Y Beeson; P V Benos; B P Berman; D Bhandari; S Bolshakov; D Borkova; M R Botchan; J Bouck; P Brokstein; P Brottier; K C Burtis; D A Busam; H Butler; E Cadieu; A Center; I Chandra; J M Cherry; S Cawley; C Dahlke; L B Davenport; P Davies; B de Pablos; A Delcher; Z Deng; A D Mays; I Dew; S M Dietz; K Dodson; L E Doup; M Downes; S Dugan-Rocha; B C Dunkov; P Dunn; K J Durbin; C C Evangelista; C Ferraz; S Ferriera; W Fleischmann; C Fosler; A E Gabrielian; N S Garg; W M Gelbart; K Glasser; A Glodek; F Gong; J H Gorrell; Z Gu; P Guan; M Harris; N L Harris; D Harvey; T J Heiman; J R Hernandez; J Houck; D Hostin; K A Houston; T J Howland; M H Wei; C Ibegwam; M Jalali; F Kalush; G H Karpen; Z Ke; J A Kennison; K A Ketchum; B E Kimmel; C D Kodira; C Kraft; S Kravitz; D Kulp; Z Lai; P Lasko; Y Lei; A A Levitsky; J Li; Z Li; Y Liang; X Lin; X Liu; B Mattei; T C McIntosh; M P McLeod; D McPherson; G Merkulov; N V Milshina; C Mobarry; J Morris; A Moshrefi; S M Mount; M Moy; B Murphy; L Murphy; D M Muzny; D L Nelson; D R Nelson; K A Nelson; K Nixon; D R Nusskern; J M Pacleb; M Palazzolo; G S Pittman; S Pan; J Pollard; V Puri; M G Reese; K Reinert; K Remington; R D Saunders; F Scheeler; H Shen; B C Shue; I Sidén-Kiamos; M Simpson; M P Skupski; T Smith; E Spier; A C Spradling; M Stapleton; R Strong; E Sun; R Svirskas; C Tector; R Turner; E Venter; A H Wang; X Wang; Z Y Wang; D A Wassarman; G M Weinstock; J Weissenbach; S M Williams; K C Worley; D Wu; S Yang; Q A Yao; J Ye; R F Yeh; J S Zaveri; M Zhan; G Zhang; Q Zhao; L Zheng; X H Zheng; F N Zhong; W Zhong; X Zhou; S Zhu; X Zhu; H O Smith; R A Gibbs; E W Myers; G M Rubin; J C Venter
Journal:  Science       Date:  2000-03-24       Impact factor: 47.728

  10 in total
  1523 in total

1.  Role of OsNPR1 in rice defense program as revealed by genome-wide expression analysis.

Authors:  Shoji Sugano; Chang-Jie Jiang; Shin-Ichi Miyazawa; Chisato Masumoto; Katsumi Yazawa; Nagao Hayashi; Masaki Shimono; Akira Nakayama; Mitsue Miyao; Hiroshi Takatsuji
Journal:  Plant Mol Biol       Date:  2010-10-07       Impact factor: 4.076

2.  Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs.

Authors:  Gozde Kar; Ozlem Keskin; Ruth Nussinov; Attila Gursoy
Journal:  J Proteome Res       Date:  2012-01-10       Impact factor: 4.466

3.  Deciphering the Arabidopsis floral transition process by integrating a protein-protein interaction network and gene expression data.

Authors:  Fei He; Yuan Zhou; Ziding Zhang
Journal:  Plant Physiol       Date:  2010-06-07       Impact factor: 8.340

4.  A Novel Schema to Enhance Data Quality of Patient Safety Event Reports.

Authors:  Hong Kang; Yang Gong
Journal:  AMIA Annu Symp Proc       Date:  2017-02-10

5.  Proteomic identification of novel plasma kallikrein substrates in the astrocyte secretome.

Authors:  Jia Liu; Ben-Bo Gao; Edward P Feener
Journal:  Transl Stroke Res       Date:  2010-08-28       Impact factor: 6.829

6.  Discrimination between adenocarcinoma and normal pancreatic ductal fluid by proteomic and glycomic analysis.

Authors:  Mindy Porterfield; Peng Zhao; Haiyong Han; John Cunningham; Kazuhiro Aoki; Daniel D Von Hoff; Michael J Demeure; J Michael Pierce; Michael Tiemeyer; Lance Wells
Journal:  J Proteome Res       Date:  2013-12-12       Impact factor: 4.466

7.  The mouse Gene Expression Database (GXD): updates and enhancements.

Authors:  David P Hill; Dale A Begley; Jacqueline H Finger; Terry F Hayamizu; Ingeborg J McCright; Constance M Smith; Jon S Beal; Lori E Corbani; Judith A Blake; Janan T Eppig; James A Kadin; Joel E Richardson; Martin Ringwald
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

8.  Transcriptome profiling and functional analysis of Agrobacterium tumefaciens reveals a general conserved response to acidic conditions (pH 5.5) and a complex acid-mediated signaling involved in Agrobacterium-plant interactions.

Authors:  Ze-Chun Yuan; Pu Liu; Panatda Saenkham; Kathleen Kerr; Eugene W Nester
Journal:  J Bacteriol       Date:  2007-11-09       Impact factor: 3.490

9.  Constraint and turnover in sex-biased gene expression in the genus Drosophila.

Authors:  Yu Zhang; David Sturgill; Michael Parisi; Sudhir Kumar; Brian Oliver
Journal:  Nature       Date:  2007-11-08       Impact factor: 49.962

10.  Comparison of nanotube-protein corona composition in cell culture media.

Authors:  Jonathan H Shannahan; Jared M Brown; Ran Chen; Pu Chun Ke; Xianyin Lai; Somenath Mitra; Frank A Witzmann
Journal:  Small       Date:  2013-01-16       Impact factor: 13.281

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