Results 31 to 40 of about 169 (169)

Gene Ontology Consortium: going forward [PDF]

Nucleic Acids Research, 2014
The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently ...
Consortium, Gene Ontology, Blake, Judith A, Christie, Karen R, Dolan, Mary E, Drabkin, Harold J, Hill, David P, Ni, Li, Sitnikov, Dmitry   +7 more
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The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology [PDF]

Nucleic Acids Research, 2004
The Gene Ontology Annotation (GOA) database (http://www.ebi.ac.uk/GOA) aims to provide high-quality electronic and manual annotations to the UniProt Knowledgebase (Swiss-Prot, TrEMBL and PIR-PSD) using the standardized vocabulary of the Gene Ontology (GO).
Michele Magrane, Rodrigo Lopez, Nicola Harte, Vivian Lee, Daniel Barrell, Emily Dimmer, John Maslen, Rolf Apweiler, Evelyn Camon, David Binns   +9 more
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The Vision and Challenges of the Gene Ontology [PDF]

, 2016
The overarching goal of the Gene Ontology (GO) Consortium is to provide researchers in biology and biomedicine with all current functional information concerning genes and the cellular context under which these occur. When the GO was started in the 1990s surprisingly little attention had been given to how functional information about genes was to be ...
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Measuring the Evolution of Ontology Complexity: The Gene Ontology Case Study [PDF]

PLoS ONE, 2013
Ontologies support automatic sharing, combination and analysis of life sciences data. They undergo regular curation and enrichment. We studied the impact of an ontology evolution on its structural complexity. As a case study we used the sixty monthly releases between January 2008 and December 2012 of the Gene Ontology and its three independent branches,
Charles Bettembourg, Charles Bettembourg, Charles Bettembourg, Olivier Dameron, Olivier Dameron, Nolwenn Le Meur, Nolwenn Le Meur   +6 more
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Sequence Ontology terminology for gene regulation

Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2021
The Sequence Ontology (SO) is a structured, controlled vocabulary that provides terms and definitions for genomic annotation. The Gene Regulation Ensemble Effort for the Knowledge Commons (GREEKC) initiative has gathered input from many groups of researchers, including the SO, the Gene Ontology (GO), and gene regulation experts, with the goal of ...
Christopher J. Mungall, Karen Eilbeck, Michael Sinclair, Daniel R. Zerbino, Colin Logie, Stefan Schulz, Ruth C. Lovering, David W. Sant, David W. Sant   +8 more
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Gene Ontology: Pitfalls, Biases, and Remedies [PDF]

, 2016
The Gene Ontology (GO) is a formidable resource but there are several considerations about it that are essential to understand the data and interpret it correctly. The GO is sufficiently simple that it can be used without deep understanding of its structure or how it is developed, which is both a strength and a weakness.
Christophe Dessimoz, Christophe Dessimoz, Christophe Dessimoz, Pascale Gaudet   +3 more
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Extending gene ontology with gene association networks [PDF]

Bioinformatics, 2015
Abstract Motivation: Gene ontology (GO) is a widely used resource to describe the attributes for gene products. However, automatic GO maintenance remains to be difficult because of the complex logical reasoning and the need of biological knowledge that are not explicitly represented in the GO.
Jiajie Peng, Jiajie Peng, Jixuan Wang, Jin Chen, Yadong Wang, Tao Wang   +5 more
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Multidimensional OMICs reveal ARID1A orchestrated control of DNA damage, splicing, and cell cycle in normal‐like and malignant urothelial cells

Molecular Oncology, EarlyView.
Loss of the frequently mutated chromatin remodeler ARID1A, a subunit of the SWI/SNF cBAF complex, results in less open chromatin, alternative splicing, and the failure to stop cells from progressing through the cell cycle after DNA damage in bladder (cancer) cells. Created in BioRender. Epigenetic regulators, such as the SWI/SNF complex, with important
Rebecca M. Schlösser, Florian Krumbach, Eyleen Corrales, Geoffroy Andrieux, Christian Preisinger, Franziska Liss, Alexandra Golzmann, Melanie Boerries, Kerstin Becker, Ruth Knüchel, Stefan Garczyk, Bernhard Lüscher   +11 more
wiley   +1 more source

Escape from TGF‐β‐induced senescence promotes aggressive hallmarks in epithelial hepatocellular carcinoma cells

Molecular Oncology, EarlyView.
Chronic TGF‐β exposure drives epithelial HCC cells from a senescent state to a TGF‐β resistant mesenchymal phenotype. This transition is characterized by the loss of Smad3‐mediated signaling, escape from senescence, enhanced invasiveness and metastatic potential, and upregulation of key resistance modulators such as MARK1 and GRM8, ultimately promoting
Minenur Kalyoncu, Dilara Demirci, Sude Eris, Bengisu Dayanc, Ece Cakiroglu, Merve Basol, Merve Uysal, Gulcin Cakan‐Akdogan, Fang Liu, Mehmet Ozturk, Gökhan Karakülah, Serif Senturk   +11 more
wiley   +1 more source

Testing for treatment effects on gene ontology [PDF]

BMC Bioinformatics, 2008
In studies that use DNA arrays to assess changes in gene expression, it is preferable to measure the significance of treatment effects on a group of genes from a pathway or functional category such as gene ontology terms (GO terms, http://www.geneontology.org) because this facilitates the interpretation of effects and may markedly increase significance.
Robert J. Shmookler Reis, Taewon Lee, Cruz Velasco, Varsha G. Desai, Robert R. Delongchamp   +4 more
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