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The Gene Ontology knowledgebase in 2023. [PDF]

Genetics, 2023
The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs).
Gene Ontology Consortium, Aleksander SA, Balhoff J, Carbon S, Cherry JM, Drabkin HJ, Ebert D, Feuermann M, Gaudet P, Harris NL, Hill DP, Lee R, Mi H, Moxon S, Mungall CJ, Muruganugan A, Mushayahama T, Sternberg PW, Thomas PD, Van Auken K, Ramsey J, Siegele DA, Chisholm RL, Fey P, Aspromonte MC, Nugnes MV, Quaglia F, Tosatto S, Giglio M, Nadendla S, Antonazzo G, Attrill H, Dos Santos G, Marygold S, Strelets V, Tabone CJ, Thurmond J, Zhou P, Ahmed SH, Asanitthong P, Luna Buitrago D, Erdol MN, Gage MC, Ali Kadhum M, Li KYC, Long M, Michalak A, Pesala A, Pritazahra A, Saverimuttu SCC, Su R, Thurlow KE, Lovering RC, Logie C, Oliferenko S, Blake J, Christie K, Corbani L, Dolan ME, Drabkin HJ, Hill DP, Ni L, Sitnikov D, Smith C, Cuzick A, Seager J, Cooper L, Elser J, Jaiswal P, Gupta P, Jaiswal P, Naithani S, Lera-Ramirez M, Rutherford K, Wood V, De Pons JL, Dwinell MR, Hayman GT, Kaldunski ML, Kwitek AE, Laulederkind SJF, Tutaj MA, Vedi M, Wang SJ, D'Eustachio P, Aimo L, Axelsen K, Bridge A, Hyka-Nouspikel N, Morgat A, Aleksander SA, Cherry JM, Engel SR, Karra K, Miyasato SR, Nash RS, Skrzypek MS, Weng S, Wong ED, Bakker E, Berardini TZ, Reiser L, Auchincloss A, Axelsen K, Argoud-Puy G, Blatter MC, Boutet E, Breuza L, Bridge A, Casals-Casas C, Coudert E, Estreicher A, Livia Famiglietti M, Feuermann M, Gos A, Gruaz-Gumowski N, Hulo C, Hyka-Nouspikel N, Jungo F, Le Mercier P, Lieberherr D, Masson P, Morgat A, Pedruzzi I, Pourcel L, Poux S, Rivoire C, Sundaram S, Bateman A, Bowler-Barnett E, Bye-A-Jee H, Denny P, Ignatchenko A, Ishtiaq R, Lock A, Lussi Y, Magrane M, Martin MJ, Orchard S, Raposo P, Speretta E, Tyagi N, Warner K, Zaru R, Diehl AD, Lee R, Chan J, Diamantakis S, Raciti D, Zarowiecki M, Fisher M, James-Zorn C, Ponferrada V, Zorn A, Ramachandran S, Ruzicka L, Westerfield M.   +156 more
europepmc   +10 more sources

Expansion of the Gene Ontology knowledgebase and resources [PDF]

Nucleic Acids Res., 2016
The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data.
The Gene Ontology Consortium, .
core   +2 more sources

rrvgo: a Bioconductor package for interpreting lists of Gene Ontology terms. [PDF]

MicroPubl Biol, 2023
Gene Ontology (GO) annotation is often used to guide the biological interpretation of high-throughput omics experiments, e.g. by analysing lists of differentially regulated genes for enriched GO terms. Due to the hierarchical nature of GOs, the resulting
Sayols S.
europepmc   +2 more sources

CirGO: an alternative circular way of visualising gene ontology terms

BMC Bioinformatics, 2019
Background Prioritisation of gene ontology terms from differential gene expression analyses in a two-dimensional format remains a challenge with exponentially growing data volumes.
Irina Kuznetsova, Artur Lugmayr, Stefan J. Siira, Oliver Rackham, Aleksandra Filipovska   +4 more
doaj   +2 more sources

Capturing heart valve development with Gene Ontology [PDF]

Frontiers in Genetics, 2023
Introduction: The normal development of all heart valves requires highly coordinated signaling pathways and downstream mediators. While genomic variants can be responsible for congenital valve disease, environmental factors can also play a role. Later in
Saadullah H. Ahmed, Alexander T. Deng, Rachael P. Huntley, Nancy H. Campbell, Ruth C. Lovering   +4 more
doaj   +2 more sources

A Bayesian Hierarchical Model to Derive Novel Gene Networks from Gene Ontology Fingerprints [PDF]

, 2009
We developed a Bayesian hierarchical model to identify gene networks based on the similarity score generated from comparing the gene ontology fingerprints of gene pairs.
Tingting Qin, Lam C. Tsoi, Andrew Lawson, Jim Zheng   +3 more
openalex   +4 more sources

Gene Ontology Meta Annotator for Plants (GOMAP)

Plant Methods, 2021
Annotating gene structures and functions to genome assemblies is necessary to make assembly resources useful for biological inference. Gene Ontology (GO) term assignment is the most used functional annotation system, and new methods for GO assignment ...
Kokulapalan Wimalanathan, Carolyn J. Lawrence-Dill   +1 more
doaj   +2 more sources

Identifying term relations cross different gene ontology categories [PDF]

BMC Bioinformatics, 2017
The Gene Ontology (GO) is a community-based bioinformatics resource that employs ontologies to represent biological knowledge and describes information about gene and gene product function.
Jiajie Peng, Honggang Wang, Junya Lu, Weiwei Hui, Yadong Wang, Xuequn Shang   +5 more
openalex   +2 more sources

Combining gene ontology with deep neural networks to enhance the clustering of single cell RNA-Seq data

BMC Bioinformatics, 2019
Background Single cell RNA sequencing (scRNA-seq) is applied to assay the individual transcriptomes of large numbers of cells. The gene expression at single-cell level provides an opportunity for better understanding of cell function and new discoveries ...
Jiajie Peng, Xiaoyu Wang, Xuequn Shang
doaj   +2 more sources

The Functional Genetics of Handedness and Language Lateralization: Insights from Gene Ontology, Pathway and Disease Association Analyses

Frontiers in Psychology, 2017
Handedness and language lateralization are partially determined by genetic influences. It has been estimated that at least 40 (and potentially more) possibly interacting genes may influence the ontogenesis of hemispheric asymmetries.
Judith Schmitz, Stephanie Lor, Rena Klose, Onur Güntürkün, Sebastian Ocklenburg   +4 more
doaj   +2 more sources