Search

Your search keyword '"Saverimuttu SCC"' showing total 2 results
Start Over Author "Saverimuttu SCC" Topic gene ontology
2 results on '"Saverimuttu SCC"'

1. Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data.

Author

Kramarz B, Huntley RP, Rodríguez-López M, Roncaglia P, Saverimuttu SCC, Parkinson H, Bandopadhyay R, Martin MJ, Orchard S, Hooper NM, Brough D, and Lovering RC

Subjects
Computational Biology methods, Humans, Microglia metabolism, Molecular Sequence Annotation methods, Alzheimer Disease genetics, Encephalitis genetics, Gene Expression, Gene Ontology
Abstract

Background: Gene Ontology (GO) is a major bioinformatic resource used for analysis of large biomedical datasets, for example from genome-wide association studies, applied universally across biological fields, including Alzheimer's disease (AD) research., Objective: We aim to demonstrate the applicability of GO for interpretation of AD datasets to improve the understanding of the underlying molecular disease mechanisms, including the involvement of inflammatory pathways and dysregulated microRNAs (miRs)., Methods: We have undertaken a systematic full article GO annotation approach focused on microglial proteins implicated in AD and the miRs regulating their expression. PANTHER was used for enrichment analysis of previously published AD data. Cytoscape was used for visualizing and analyzing miR-target interactions captured from published experimental evidence., Results: We contributed 3,084 new annotations for 494 entities, i.e., on average six new annotations per entity. This included a total of 1,352 annotations for 40 prioritized microglial proteins implicated in AD and 66 miRs regulating their expression, yielding an average of twelve annotations per prioritized entity. The updated GO resource was then used to re-analyze previously published data. The re-analysis showed novel processes associated with AD-related genes, not identified in the original study, such as 'gliogenesis', 'regulation of neuron projection development', or 'response to cytokine', demonstrating enhanced applicability of GO for neuroscience research., Conclusions: This study highlights ongoing development of the neurobiological aspects of GO and demonstrates the value of biocuration activities in the area, thus helping to delineate the molecular bases of AD to aid the development of diagnostic tools and treatments.

Published
2020
Full Text
View/download PDF

2. The Gene Ontology resource: enriching a GOld mine

Author

Carbon, S, Douglass, E, Good, Bm, Unni, Dr, Harris, Nl, Mungall, Cj, Basu, S, Chisholm, Rl, Dodson, Rj, Hartline, E, Fey, P, Thomas, Pd, Albou, Lp, Ebert, D, Kesling, Mj, Mi, Hy, Muruganujan, A, Huang, Xs, Mushayahama, T, Labonte, Sa, Siegele, Da, Antonazzo, G, Attrill, H, Brown, Nh, Garapati, P, Marygold, Sj, Trovisco, V, Dos Santos, G, Falls, K, Tabone, C, Zhou, Pl, Goodman, Jl, Strelets, Vb, Thurmond, J, Garmiri, P, Ishtiaq, R, Rodriguez-Lopez, M, Acencio, Ml, Kuiper, M, Laegreid, A, Logie, C, Lovering, Rc, Kramarz, B, Saverimuttu, Scc, Pinheiro, Sm, Gunn, H, Su, Rz, Thurlow, Ke, Chibucos, M, Giglio, M, Nadendla, S, Munro, J, Jackson, R, Duesbury, Mj, Del-Toro, N, Meldal, Bhm, Paneerselvam, K, Perfetto, L, Porras, P, Orchard, S, Shrivastava, A, Chang, Hy, Finn, Rd, Mitchell, Al, Rawlings, Nd, Richardson, L, Sangrador-Vegas, A, Blake, Ja, Christie, Kr, Dolan, Me, Drabkin, Hj, Hill, Dp, Ni, L, Sitnikov, Dm, Harris, Ma, Oliver, Sg, Rutherford, K, Wood, V, Hayles, J, Bahler, J, Bolton, Er, De Pons JL, Dwinell, Mr, Hayman, Gt, Kaldunski, Ml, Kwitek, Ae, Laulederkind, Sjf, Plasterer, C, Tutaj, Ma, Vedi, M, Wang, Sj, D'Eustachio, P, Matthews, L, Balhoff, Jp, Aleksander, Sa, Alexander, Mj, Cherry, Jm, Engel, Sr, Gondwe, F, Karra, K, Miyasato, Sr, Nash, Rs, Simison, M, Skrzypek, Ms, Weng, S, Wong, Ed, Feuermann, M, Gaudet, P, Morgat, A, Bakker, E, Berardini, Tz, Reiser, L, Subramaniam, S, Huala, E, Arighi, Cn, Auchincloss, A, Axelsen, K, Argoud-Puy, G, Bateman, A, Blatter, Mc, Boutet, E, Bowler, E, Breuza, L, Bridge, A, Britto, R, Bye-A-Jee, H, Casas, Cc, Coudert, E, Denny, P, Estreicher, A, Famiglietti, Ml, Georghiou, G, Gos, A, Gruaz-Gumowski, N, Hatton-Ellis, E, Hulo, C, Ignatchenko, A, Jungo, F, Laiho, K, Le Mercier, P, Lieberherr, D, Lock, A, Lussi, Y, Macdougall, A, Magrane, M, Martin, Mj, Masson, P, Natale, Da, Hyka-Nouspikel, N, Pedruzzi, I, Pourcel, L, Poux, S, Pundir, S, Rivoire, C, Speretta, E, Sundaram, S, Tyagi, N, Warner, K, Zaru, R, Wu, Ch, Diehl, Ad, Chan, Jn, Grove, C, Lee, Ryn, Muller, Hm, Raciti, D, Van Auken, K, Sternberg, Pw, Berriman, M, Paulini, M, Howe, K, Gao, S, Wright, A, Stein, L, Howe, Dg, Toro, S, Westerfield, M, Jaiswal, P, Cooper, L, and Elser, J

Subjects
Traceability, AcademicSubjects/SCI00010, Arabidopsis, Saccharomyces cerevisiae, Biology, Ontology (information science), Gene Ontology, Data curation, GO-CAMs, World Wide Web, Mice, User-Computer Interface, 03 medical and health sciences, Consistency (database systems), Annotation, 0302 clinical medicine, Documentation, Resource (project management), Schema (psychology), Schizosaccharomyces, Escherichia coli, Genetics, Database Issue, Animals, Humans, Dictyostelium, Caenorhabditis elegans, Molecular Biology, Zebrafish, 030304 developmental biology, Internet, 0303 health sciences, Molecular Sequence Annotation, File format, Rats, Drosophila melanogaster, 030217 neurology & neurosurgery
Abstract

The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium over the past two years. The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs. In addition, we describe the impacts of several collaborations to refine GO and report a 10% increase in the number of GO annotations, a 25% increase in annotated gene products, and over 9,400 new scientific articles annotated. As the project matures, we continue our efforts to review older annotations in light of newer findings, and, to maintain consistency with other ontologies. As a result, 20 000 annotations derived from experimental data were reviewed, corresponding to 2.5% of experimental GO annotations. The website (http://geneontology.org) was redesigned for quick access to documentation, downloads and tools. To maintain an accurate resource and support traceability and reproducibility, we have made available a historical archive covering the past 15 years of GO data with a consistent format and file structure for both the ontology and annotations.

Published
2021

Catalog

Books, media, physical & digital resources
See catalog results