Results 121 to 130 of about 7,457,987 (378)

Cross-Product Extensions of the Gene Ontology [PDF]

, 2009
The Gene Ontology is being normalized and extended to include computable logical definitions. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry ontologies.
Amelia Ireland, Christopher J. Mungall, David P. Hill, Jane Lomax, Jennifer Deegan, Michael Bada, Midori A. Harris, Tanya Z. Berardini   +7 more
core   +1 more source

Molecular characterisation of human penile carcinoma and generation of paired epithelial primary cell lines

Molecular Oncology, EarlyView.
Generation of two normal and tumour (cancerous) paired human cell lines using an established tissue culture technique and their characterisation is described. Cell lines were characterised at cellular, protein, chromosome and gene expression levels and for HPV status.
Simon Broad, Mahmood Hachim, Tom Bertin, Karolina Penderecka, Rifat Hamoudi, Saif Khan, Rui Henrique, Natalie Bergmoser, Manit Arya, Kalle Sipila, Matteo Vietri Rudan, Asif Muneer, Aamir Ahmed   +12 more
wiley   +1 more source

Functional abstraction as a method to discover knowledge in gene ontologies.

PLoS ONE, 2014
Computational analyses of functions of gene sets obtained in microarray analyses or by topical database searches are increasingly important in biology. To understand their functions, the sets are usually mapped to Gene Ontology knowledge bases by means ...
Alfred Ultsch, Jörn Lötsch
doaj   +1 more source

Using Ontology Fingerprints to evaluate genome-wide association study results [PDF]

, 2009
We describe an approach to characterize genes or phenotypes via ontology fingerprints which are composed of Gene Ontology (GO) terms overrepresented among those PubMed abstracts linked to the genes or phenotypes. We then quantify the biological relevance
Lam C. Tsoi, Michael Boehnke, Richard L. Klein, W. Jim Zheng   +3 more
core   +1 more source

Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach

BMC Systems Biology, 2018
BackgroundGene Ontology (GO) is one of the most popular bioinformatics resources. In the past decade, Gene Ontology-based gene semantic similarity has been effectively used to model gene-to-gene interactions in multiple research areas.
Jiajie Peng, Xuanshuo Zhang, Weiwei Hui, Junya Lu, Qianqian Li, Shuhui Liu, Xuequn Shang   +6 more
semanticscholar   +1 more source

Biological Profiling of Gene Groups utilizing Gene Ontology

Genome informatics. International Conference on Genome Informatics, 2004
Increasingly used high throughput experimental techniques, like DNA or protein microarrays give as a result groups of interesting, e.g. differentially regulated genes which require further biological interpretation. With the systematic functional annotation provided by the Gene Ontology the information required to automate the interpretation task is ...
Blüthgen, Nils, Brand, Karsten, Čajavec, Branka, Swat, Maciej, Herzel, Hanspeter, Beule, Dieter   +5 more
openaire   +3 more sources

Transcriptional network analysis of PTEN‐protein‐deficient prostate tumors reveals robust stromal reprogramming and signs of senescent paracrine communication

Molecular Oncology, EarlyView.
Combining PTEN protein assessment and transcriptomic profiling of prostate tumors, we uncovered a network enriched in senescence and extracellular matrix (ECM) programs associated with PTEN loss and conserved in a mouse model. We show that PTEN‐deficient cells trigger paracrine remodeling of the surrounding stroma and this information could help ...
Ivana Rondon‐Lorefice, Jose I. Lopez, Aitziber Ugalde‐Olano, Maite Zufiaurre, Ianire Astobiza, Natalia Martin‐Martin, Laura Bozal‐Basterra, Saioa Garcia‐Longarte, Amaia Zabala‐Letona, Sofia Rey, Aida Santos‐Martin, Miguel Unda, Ana Loizaga‐Iriarte, Mariona Graupera, Paolo Nuciforo, Arkaitz Carracedo, Isabel Mendizabal   +16 more
wiley   +1 more source

Using philosophy to improve the coherence and interoperability of applications ontologies: A field report on the collaboration of IFOMIS and L&C [PDF]

, 2004
The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the
Fielding, James Matthew, Simon, Jonathan, Smith, Barry   +2 more
core  

Gene expression patterns in anterior pituitary associated with quantitative measure of oestrous behaviour in dairy cows [PDF]

, 2010
Intensive selection for high milk yield in dairy cows has raised production levels substantially but at the cost of reduced fertility, which manifests in different ways including reduced expression of oestrous behaviour.
Beerda, B., Frijters, A.C.J., Kommadath, A., Mulder, H.A., Pas, M.F.W., te, Smits, M.A., Veerkamp, R.F., Wit, A.A.C., de, Woelders, H.   +8 more
core   +2 more sources

Gene ontology analysis for RNA-seq: accounting for selection bias

Genome Biology, 2010
We present GOseq, an application for performing Gene Ontology (GO) analysis on RNA-seq data. GO analysis is widely used to reduce complexity and highlight biological processes in genome-wide expression studies, but standard methods give biased results on
Matthew D. Young, Matthew J. Wakefield, Gordon K. Smyth, Alicia Oshlack   +3 more
semanticscholar   +1 more source