Results 31 to 40 of about 308,702 (255)

Mining the Gene Wiki for functional genomic knowledge

BMC Genomics, 2011
Background Ontology-based gene annotations are important tools for organizing and analyzing genome-scale biological data. Collecting these annotations is a valuable but costly endeavor.
Good Benjamin M, Howe Douglas G, Lin Simon M, Kibbe Warren A, Su Andrew I   +4 more
doaj   +1 more source

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.

PLoS Computational Biology, 2012
A recent paper (Nehrt et al., PLoS Comput. Biol. 7:e1002073, 2011) has proposed a metric for the "functional similarity" between two genes that uses only the Gene Ontology (GO) annotations directly derived from published experimental results.
Paul D Thomas, Valerie Wood, Christopher J Mungall, Suzanna E Lewis, Judith A Blake, Gene Ontology Consortium   +5 more
doaj   +1 more source

The Gene Ontology: enhancements for 2011 [PDF]

Nucleic Acids Research, 2011
The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of GO annotations of gene products has increased due to curation efforts among GO Consortium (GOC) groups, including focused literature-based annotation and ...
Chan, J., Kishore, R., Sternberg, P., Van Auken, K., Gene Ontology Consortium   +4 more
openaire   +6 more sources

Construction of ontology augmented networks for protein complex prediction.

PLoS ONE, 2013
Protein complexes are of great importance in understanding the principles of cellular organization and function. The increase in available protein-protein interaction data, gene ontology and other resources make it possible to develop computational ...
Yijia Zhang, Hongfei Lin, Zhihao Yang, Jian Wang   +3 more
doaj   +1 more source

Disjunctive shared information between ontology concepts: application to Gene Ontology

Journal of Biomedical Semantics, 2011
Background The large-scale effort in developing, maintaining and making biomedical ontologies available motivates the application of similarity measures to compare ontology concepts or, by extension, the entities described therein.
Couto Francisco M, Silva Mário J
doaj   +1 more source

Functional-network-based gene set analysis using gene-ontology. [PDF]

PLoS ONE, 2013
To account for the functional non-equivalence among a set of genes within a biological pathway when performing gene set analysis, we introduce GOGANPA, a network-based gene set analysis method, which up-weights genes with functions relevant to the gene ...
Billy Chang, Rafal Kustra, Weidong Tian
doaj   +1 more source

Gene function prediction based on the Gene Ontology hierarchical structure. [PDF]

PLoS ONE, 2014
The information of the Gene Ontology annotation is helpful in the explanation of life science phenomena, and can provide great support for the research of the biomedical field.
Liangxi Cheng, Hongfei Lin, Yuncui Hu, Jian Wang, Zhihao Yang   +4 more
doaj   +1 more source

Onion Extract on Cell Gene Expression Profile: a System Biology Approach [PDF]

Research Journal of Pharmacognosy, 2023
Background and objectives: Widespread consuming of onion as a nutrient in the world implies more investigations about useful and harmful aspects of this common supplementary food.
Babak Arjmand, Somayeh Jahani Sherafat, Mostafa Rezaei Tavirani*, Alireza Ahmadzadeh, Mona Zamanian-Azodi, Mahmood Khodadoost   +5 more
doaj   +1 more source

Length bias correction in gene ontology enrichment analysis using logistic regression. [PDF]

PLoS ONE, 2012
When assessing differential gene expression from RNA sequencing data, commonly used statistical tests tend to have greater power to detect differential expression of genes encoding longer transcripts. This phenomenon, called "length bias", will influence
Gu Mi, Yanming Di, Sarah Emerson, Jason S Cumbie, Jeff H Chang   +4 more
doaj   +1 more source

The Gene Ontology project in 2008 [PDF]

Nucleic Acids Research, 2007
The Gene Ontology (GO) project (http://www.geneontology.org/) provides a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://www.sequenceontology.org/). The ontologies have been extended and refined for several biological areas, and improvements to the structure of the ...
Harris, Midori A, Deegan, Jennifer I., Ireland, Amelia, Lomax, Jane, Ashburner, Michael, Tweedie, Susan, Carbon, Seth, Lewis, Suzanna, Mungall, Chris, Day Richter, John, Eilbeck, Karen, Blake, Judith A., Bult, Carol, Diehl, Alexander D., Dolan, Mary, Drabkin, Harold, Eppig, Janan T., Hill, David P., Ni, Li, Ringwald, Martin, Balakrishnan, Rama, Binkley, Gail, Cherry, J. Michael, Christie, Karen R., Costanzo, Maria C., Dong, Qing, Engel, Stacia R., Fisk, Dianna G., Hirschman, Jodi E., Hitz, Benjamin C., Hong, Eurie L., Krieger, Cynthia J., Miyasato, Stuart R., Nash, Robert S., Park, Julie, Skrzypek, Marek S., Weng, Shuai, Wong, Edith D., Zhu, Kathy K., Botstein, David, Dolinski, Kara, Livstone, Michael S., Oughtred, Rose, Berardini, Tanya, Li, Donghui, Rhee, Seung Y., Apweiler, Rolf, Barrell, Daniel, Camon, Evelyn, Dimmer, Emily, Huntley, Rachael, Mulder, Nicola, Khodiyar, Varsha K., Lovering, Ruth C., Povey, Sue, Chisholm, Rex, Fey, Petra, Gaudet, Pascale, Kibbe, Warren, Kishore, Ranjana, Schwarz, Erich M., Sternberg, Paul, Van Auken, Kimberly, Giglio, Michelle Gwinn, Hannick, Linda, Wortman, Jennifer, Aslett, Martin, Berriman, Matthew, Wood, Valerie, Jacob, Howard, Laulederkind, Stan, Petri, Victoria, Shimoyama, Mary, Smith, Jennifer, Twigger, Simon, Jaiswal, Pankaj, Seigfried, Trent, Howe, Doug, Westerfield, Monte, Collmer, Candace, Torto Alalibo, Trudy, FELTRIN, ERIKA, VALLE, GIORGIO, Bromberg, Susan, Burgess, Shane, Mccarthy, Fiona   +85 more
openaire   +3 more sources