Access the full text.
Sign up today, get DeepDyve free for 14 days.
T Hubbard, D Andrews, M Caccamo (2004)
Ensembl 2005Nucleic Acids Res, 33
Glynn Dennis, Brad Sherman, Douglas Hosack, Jun Yang, Wei Gao, H. Lane, R. Lempicki (2003)
DAVID: Database for Annotation, Visualization, and Integrated DiscoveryGenome Biology, 4
L. Martínez-Cruz, Á. Rubio, M. Martínez‐Chantar, A. Labarga, Isabel Barrio, A. Podhorski, V. Segura, José Campo, M. Ávila, J. Mato (2003)
GARBAN: genomic analysis and rapid biological annotation of cDNA microarray and proteomic dataBioinformatics, 19 16
M Ashbumer, C Ball, J Blake (2000)
Gene ontology: tool for the unification of biology. The Gene Ontology ConsortiumNat Genet, 25
C. Bean, R. Green (2001)
Relationships in the Organization of Knowledge
J. Fink, Scott Drewes, Hiren Patel, J. Welsh, D. Masys, J. Corbeil, M. Gribskov (2003)
2HAPI: A Microarray Data Analysis SystemBioinformatics, 19 11
K. Pruitt, D. Maglott (2001)
RefSeq and LocusLink: NCBI gene-centered resourcesNucleic acids research, 29 1
R Gentleman, D Scholtens, B Ding (2005)
Bioinformatics and computational biology solutions using R and bioconductor
B. Rihn, Solveig Vidal, Claude Nemurat, S. Vachenc, S. Mohr, Florian Mazur, Philippe Houdry, F. Grandjean, S. Visvikis, Jacques Ducloy (2003)
From transcriptomics to bibliomics.Medical science monitor : international medical journal of experimental and clinical research, 9 8
K. Cheung, R. Knikker, Youjun Guo, Guoneng Zhong, Janet Hager, Kevin Yip, A. Kwan, P. Li, D. Cheung (2004)
BiosphereApplied Bioinformatics, 3
M. Harris, Jennifer Clark, A. Ireland, J. Lomax, M. Ashburner, M. Ashburner, R. Foulger, R. Foulger, K. Eilbeck, K. Eilbeck, S. Lewis, S. Lewis, B. Marshall, B. Marshall, C. Mungall, C. Mungall, J. Richter, J. Richter, G. Rubin, Gerald Rubin, J. Blake, C. Bult, M. Dolan, H. Drabkin, J. Eppig, Hill Dp, L. Ni, M. Ringwald, R. Balakrishnan, R. Balakrishnan, J. Cherry, J. Cherry, K. Christie, K. Christie, M. Costanzo, M. Costanzo, S. Dwight, S. Dwight, S. Engel, S. Engel, D. Fisk, D. Fisk, J. Hirschman, J. Hirschman, Eurie Hong, Eurie Hong, R. Nash, R. Nash, A. Sethuraman, A. Sethuraman, C. Theesfeld, C. Theesfeld, D. Botstein, D. Botstein, K. Dolinski, K. Dolinski, B. Feierbach, B. Feierbach, T. Berardini, T. Berardini, S. Mundodi, S. Mundodi, S. Rhee, S. Rhee, R. Apweiler, D. Barrell, E. Camon, E. Dimmer, Lee, R. Chisholm, P. Gaudet, P. Gaudet, W. Kibbe, W. Kibbe, R. Kishore, R. Kishore, E. Schwarz, E. Schwarz, P. Sternberg, P. Sternberg, M. Gwinn, L. Hannick, J. Wortman, M. Berriman, Wood, N. Delacruz, N. Delacruz, P. Tonellato, P. Tonellato, P. Jaiswal, P. Jaiswal, T. Seigfried, T. Seigfried, R. White, R. White (2004)
Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resourceNucleic acids research, 32 Database issue
P. Khatri, S. Drăghici, G. Ostermeier, S. Krawetz (2002)
Profiling gene expression using onto-express.Genomics, 79 2
M. Ashburner, C. Ball, J. Blake, D. Botstein, Heather Butler, J. Cherry, A. Davis, K. Dolinski, S. Dwight, J. Eppig, M. Harris, D. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J. Matese, J. Richardson, M. Ringwald, G. Rubin, G. Sherlock (2000)
Gene Ontology: tool for the unification of biologyNature Genetics, 25
Donna Maglott, Kenneth Katz, Hugues Sicotte, Kim Pruitt (2000)
NCBI's LocusLink and RefSeqNucleic acids research, 28 1
A. Djebbari, S. Karamycheva, E. Howe, John Quackenbush (2005)
MeSHer: identifying biological concepts in microarray assays based on PubMed references and MeSH termsBioinformatics, 21 15
M Harris, J Clark, A Ireland (2004)
The gene ontology (GO) database and informatics resourceNucleic Acids Res, 32
G. Berriz, O. King, Barbara Bryant, C. Sander, F. Roth (2003)
Characterizing gene sets with FuncAssociateBioinformatics, 19 18
D. Masys, J. Welsh, J. Fink, M. Gribskov, Igor Klacansky, J. Corbeil (2001)
Use of keyword hierarchies to interpret gene expression patternsBioinformatics, 17 4
KH Cheung, R Knikker, Y Guo (2004)
Biosphere: the interOperation of web services in microarray cluster analysisAppl Bioinformatics, 3
R. Gentleman, V. Carey, W. Huber, R. Irizarry, S. Dudoit (2005)
Bioinformatics and Computational Biology Solutions Using R and Bioconductor (Statistics for Biology and Health)
K. Bussey, D. Kane, M. Sunshine, Sudarshan Narasimhan, S. Nishizuka, W. Reinhold, B. Zeeberg, Weinstein Ajay, J. Weinstein (2003)
MatchMiner: a tool for batch navigation among gene and gene product identifiersGenome Biology, 4
P. Schuyler, W. Hole, M. Tuttle, D. Sherertz (1993)
The UMLS Metathesaurus: representing different views of biomedical concepts.Bulletin of the Medical Library Association, 81 2
T. Hubbard, D. Barker, E. Birney, G. Cameron, Yuan Chen, Laura Clarke, Tony Cox, James Cuff, V. Curwen, T. Down, R. Durbin, E. Eyras, J. Gilbert, M. Hammond, L. Huminiecki, A. Kasprzyk, H. Lehväslaiho, P. Lijnzaad, Craig Melsopp, Emmanuel Mongin, Roger Pettett, M. Pocock, Simon Potter, A. Rust, E. Schmidt, S. Searle, G. Slater, James Smith, W. Spooner, Arne Stabenau, J. Stalker, E. Stupka, A. Ureta-Vidal, Imre Vastrik, M. Clamp (2002)
The Ensembl genome database projectNucleic acids research, 30 1
John Storey, R. Tibshirani (2003)
Statistical significance for genomewide studiesProceedings of the National Academy of Sciences of the United States of America, 100
L. Tanabe, L. Tanabe, Uwe Scherf, Larry Smith, Jae Lee, Lawrence Hunter, Lawrence Hunter, John Weinstein (1999)
MedMiner: an Internet text-mining tool for biomedical information, with application to gene expression profiling.BioTechniques, 27 6
Todd Golub, Todd Golub, D. Slonim, Pablo Tamayo, Christine Huard, Michelle Gaasenbeek, J. Mesirov, Hilary Coller, M. Loh, James Downing, Michael Caligiuri, C. Bloomfield, Eric Lander (1999)
Molecular classification of cancer: class discovery and class prediction by gene expression monitoring.Science, 286 5439
D Benson, I Karsch-Mizrachi, D Lipman (2004)
GenBankNucleic Acids Res, 33
Sheng Zhong, Lu Tian, Cheng Li, Kai-Florian Storch, W. Wong (2004)
Comparative analysis of gene sets in the gene ontology space under the multiple hypothesis testing frameworkProceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.
T. Gruber (1995)
Toward principles for the design of ontologies used for knowledge sharing?Int. J. Hum. Comput. Stud., 43
Stuart Nelson, W. Johnston, Betsy Humphreys (2001)
Relationships in Medical Subject Headings (MeSH)
A. Bairoch, R. Apweiler, Cathy Wu, W. Barker, B. Boeckmann, Serenella Ferro, E. Gasteiger, Hongzhan Huang, R. Lopez, M. Magrane, M. Martin, D. Natale, C. O’Donovan, Nicole Redaschi, L. Yeh (2004)
The Universal Protein Resource (UniProt)Nucleic Acids Research, 33
T. Harris, Nansheng Chen, Fiona Cunningham, M. Tello-Ruiz, I. Antoshechkin, C. Bastiani, Tamberlyn Bieri, Darin Blasiar, K. Bradnam, J. Chan, Chao-Kung Chen, Wen Chen, Paul Davis, Eimear Kenny, R. Kishore, D. Lawson, Raymond Lee, Hans-Michael Müller, Cecilia Nakamura, P. Ozersky, Andrei Petcherski, Anthony Rogers, A. Sabo, E. Schwarz, K. Auken, Qinghua Wang, R. Durbin, J. Spieth, P. Sternberg, L. Stein (2004)
WormBase: a multi-species resource for nematode biology and genomicsNucleic acids research, 32 Database issue
B. Zeeberg, W. Feng, Geoffrey Wang, May Wang, A. Fojo, M. Sunshine, Sudarshan Narasimhan, D. Kane, W. Reinhold, S. Lababidi, K. Bussey, J. Riss, J. Barrett, J. Weinstein (2003)
GoMiner: a resource for biological interpretation of genomic and proteomic dataGenome Biology, 4
Yongmei Ji, Xing Xu, G. Stormo (2004)
A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequencesBioinformatics, 20 10
Guoying Liu, A. Loraine, R. Shigeta, M. Cline, Jill Cheng, V. Valmeekam, Shaw Sun, D. Kulp, Michael Siani-Rose (2003)
NetAffx: Affymetrix probesets and annotationsNucleic acids research, 31 1
Sheng Zhong, Kai-Florian Storch, O. Lipan, M. Kao, C. Weitz, W. Wong (2004)
GoSurfer: a graphical interactive tool for comparative analysis of large gene sets in Gene Ontology space.Applied bioinformatics, 3 4
P. Kersey, Jorge Duarte, Allyson Williams, Youla Karavidopoulou, E. Birney, R. Apweiler (2004)
The International Protein Index: An integrated database for proteomics experimentsPROTEOMICS, 4
Bing Zhang, D. Schmoyer, S. Kirov, J. Snoddy (2004)
GOTree Machine (GOTM): a web-based platform for interpreting sets of interesting genes using Gene Ontology hierarchiesBMC Bioinformatics, 5
Cathy Wu, R. Apweiler, A. Bairoch, D. Natale, W. Barker, B. Boeckmann, Serenella Ferro, E. Gasteiger, Hongzhan Huang, R. Lopez, M. Magrane, M. Martin, R. Mazumder, C. O’Donovan, Nicole Redaschi, Baris Suzek (2005)
The Universal Protein Resource (UniProt): an expanding universe of protein informationNucleic Acids Research, 34
F. Al-Shahrour, R. Díaz-Uriarte, J. Dopazo (2004)
FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genesBioinformatics, 20 4
T. Beissbarth, T. Speed (2004)
GOstat: find statistically overrepresented Gene Ontologies within a group of genes.Bioinformatics, 20 9
P. Broberg (2005)
A comparative review of estimates of the proportion unchanged genes and the false discovery rateBMC Bioinformatics, 6
E. Camon, M. Magrane, D. Barrell, David Binns, W. Fleischmann, P. Kersey, N. Mulder, T. Oinn, J. Maslen, Anthony Cox, R. Apweiler (2003)
The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.Genome research, 13 4
R. Gentleman, D. Scholtens, B. Ding, V. Carey, W. Huber (2005)
Case Studies Using Graphs on Biological Data
C. Joslyn, S. Mniszewski, A. Fulmer, Gary Heaton (2004)
The Gene Ontology CategorizerBioinformatics, 20 Suppl 1
E. Camon, M. Magrane, D. Barrell, V. Lee, E. Dimmer, J. Maslen, David Binns, Nicola Harte, R. Lopez, R. Apweiler (2004)
The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene OntologyNucleic acids research, 32 Database issue
Gene expression and proteomics analysis allow the investigation of thousands of biomolecules in parallel. This results in a long list of interesting genes or proteins and a list of annotation terms in the order of thousands. It is not a trivial task to understand such a gene list and it would require extensive efforts to bring together the overwhelming amounts of associated information from the literature and databases. Thus, it is evident that we need ways of condensing and filtering this information. An excellent way to represent knowledge is to use ontologies, where it is possible to group genes or terms with overlapping context, rather than studying one-dimensional lists of keywords. Therefore, we have built the ontology annotation treebrowser (OAT) to represent, condense, filter and summarise the knowledge associated with a list of genes or proteins.
Applied Bioinformatics – Springer Journals
Published: Aug 22, 2012
Read and print from thousands of top scholarly journals.
Already have an account? Log in
Bookmark this article. You can see your Bookmarks on your DeepDyve Library.
To save an article, log in first, or sign up for a DeepDyve account if you don’t already have one.
Copy and paste the desired citation format or use the link below to download a file formatted for EndNote
Access the full text.
Sign up today, get DeepDyve free for 14 days.
All DeepDyve websites use cookies to improve your online experience. They were placed on your computer when you launched this website. You can change your cookie settings through your browser.