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Gene Ontology: tool for the unification of biology

Nature Genetics 25, 25 - 29 (01 May 2000). Gene Ontology: tool for the unification of biology. What is gene ontology(GO ) ?. Why do we need GO?. If you were searching for new targets for antibiotics, you might want to find. All the gene products that are :

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Gene Ontology: tool for the unification of biology

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  1. Nature Genetics 25, 25 - 29 (01 May 2000) Gene Ontology: tool for the unification of biology

  2. What is gene ontology(GO) ? Why do we need GO?

  3. If you were searching for newtargets for antibiotics, you mightwant to find...

  4. All the gene products that are: • involved in bacterial protein synthesis • significantly different sequences or structures • from those in humans. • If one database describes these molecules as being • involved in “translation”, whereas another uses the • phrase “protein synthesis” It will be difficult for you and even harder for a computer to find functionally equivalent terms.

  5. Bottleneck of biologicaldata mining • Biological data is fragmented • Biologists waste a lot of time and effort in searching for all of the available information about each small area of research. • Language used in biological research is not well controlled • Inhibit effective searching by both computers and people.

  6. The Gene Ontology (GO) • To standardize the representation of gene and gene product attributes across species and databases.

  7. Gene Ontology • GO term • Definition • Database ID • GO term: transcription initiation • Definition: Processes involved in the assembly of the RNA polymerase complex at the promoter region of a DNA template resulting in the subsequent synthesis of RNA from that promoter. • Database ID: GO:0006352

  8. Scope of GO terms • Annotated gene products (updated on 2013.12.01): • Human: 45,563 • Mouse: 25,395 • Rat: 23,219

  9. http://geneontology.org/ GO:0050975 - Perception of touch

  10. http://geneontology.org/ (A) Tooth bud initiation (B) Cellular bud initiation (C) Flower bud initiation

  11. Gene ontology project • Began as a collaboration between three model organism databases in 1998: • FlyBase (Drosophila) • Saccharomyces Genome Database (SGD) • Mouse Genome Database (MGD) • GO Consortium has grown to include many databases, including several of the world's major repositories for plant, animal and microbial genomes.

  12. How does GO work? • Three structured controlled vocabularies (GO terms) that describe gene products in terms of their associated (1) biological processes, (2) cellular components and (3) molecular functionsin a species-independent manner

  13. Cellular component: the parts of a cell or its extracellular environment • Molecular function: the elemental activities of a gene product at the molecular level, such as binding or catalysis • Biological process: operations or sets of molecular events with a defined beginning and end

  14. Molecular Function andBiological Process • A gene product may have several functions. • A function refers to a reaction or activity. • Sets of functions make up a biological process

  15. Example: GO terms for cytochrome c • Cellular component: mitochondrial matrix and mitochondrial inner membrane • Molecular function: oxidoreductase activity • Biological process: oxidative phosphorylationand induction of cell death

  16. GO terms are structured

  17. Tree view for “metaphase”

  18. Graphic view for “metaphase”

  19. What evidence is showed in GO?

  20. Find the genes involved in“chromatin organization

  21. To find the term-associated gene products

  22. References • The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat. Genet. 2000;25:25–29. • A guide to best practices for Gene Ontology (GO) manual annotation. Database (Oxford). 2013; 2013: bat054 • The Gene Ontology Consortium. Gene Ontology Annotations and Resources. Nucleic Acids Res. 2013;41:D530–D535. • The Gene Ontology Consortium. The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res. 2010;38:D331–D335. • Barrell D, Dimmer E, Huntley R, et al. The GOA database in 2009–an integrated Gene Ontology Annotation resource. Nucleic Acids Res. 2009;37:D396–D403. • MacMullen JW. Quantifying literature citations, index terms, and Gene Ontology annotations in the Saccharomyces Genome Database to assess results-set clustering utility. Proceeding of the ASIST Annual Meeting. 2006;43:1–17. • Carbon S, Ireland A, Mungall CJ, et al. AmiGO: online access to ontology and annotation data. Bioinformatics. 2009;25:288–289. • Binns D, Dimmer E, Huntley R, et al. QuickGO: a web-based tool for Gene Ontology searching. Bioinformatics. 2009;25:304–306. • Bard J, Rhee SY, Ashburner M. An ontology for cell types. Genome Biol. 2005;6:R21. • Alam-FaruqueY, Huntley RP, Khodiyar VK, et al. The impact of focused Gene Ontology curation of specific mammalian systems.

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