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Gene Ontology Project geneontology/

Use the Gene Ontology browser to search and analyze biological research data, specifically in mesoderm development and immune response. Find patterns and categorize gene products with the help of ontologies.

harryclark
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Gene Ontology Project geneontology/

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  1. Gene Ontology Project http://www.geneontology.org/

  2. There is a lot of biological research output.

  3. Search on mesoderm development…

  4. You get 6752 results! How will you ever find what you want? Another example…

  5. time Defense response Immune response Response to stimulus Toll regulated genes JAK-STAT regulated genes Puparial adhesion Molting cycle hemocyanin Amino acid catabolism Lipid metobolism Peptidase activity Protein catabloism Immune response Immune response Toll regulated genes control attacked Microarray data shows changed expression of thousands of genes. How will you spot the patterns? Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.

  6. Scientists work hard. http://www.teamtechnology.co.uk/f-scientist.jpg http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif

  7. There are lots of papers to read. http://www.teamtechnology.co.uk/f-scientist.jpg http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif

  8. More papers… http://www.teamtechnology.co.uk/f-scientist.jpg http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif

  9. more and more and more! http://www.teamtechnology.co.uk/f-scientist.jpg http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif

  10. Help! Aiuto! more and more and more! http://www.teamtechnology.co.uk/f-scientist.jpg http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif

  11. Can the computer geeks help? They are trying! http://www.newberntg.com/images/Computer-Geek-2.gif With ontologies!

  12. Ontology is a way to capture knowledge in a written and computable form.

  13. computable The computer finds patterns so we don’t have to.

  14. The Gene Ontology

  15. This is our browser.

  16. Search on mesoderm development.

  17. Here is mesoderm development.

  18. Definition of mesoderm development. Gene products involved in mesoderm development.

  19. You can read papers describing what is known about them. There are many gene products involved in mesoderm development. But fewer gene products than papers.

  20. time Defense response Immune response Response to stimulus Toll regulated genes JAK-STAT regulated genes Puparial adhesion Molting cycle hemocyanin Amino acid catabolism Lipid metobolism Peptidase activity Protein catabloism Immune response Immune response Toll regulated genes control attacked Gene Ontology can help with Microarray data. Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.

  21. time Defense response Immune response Response to stimulus Toll regulated genes JAK-STAT regulated genes Puparial adhesion Molting cycle hemocyanin Amino acid catabolism Lipid metobolism Peptidase activity Protein catabloism Immune response Immune response Toll regulated genes control attacked See which processes are upregulated or downregulated. Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.

  22. Whole genome analysis (J. D. Munkvold et al., 2004)

  23. How does the Gene Ontology work?

  24. is_a part_of Clark et al., 2005 A diagram of the whole system.

  25. The Gene Ontology is like a dictionary term: transcription initiation id: GO:0006352 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. • a name • a definition • an ID number Each concept has:

  26. The ontologies are used to categorize gene products. • Biological process ontology • Which process is a gene product involved in? • Molecular function ontology • Which molecular function does a gene product have? • Cellular component ontology • Where does a gene product act?

  27. An example… Mitochondrial P450 (CC24 PR01238; MITP450CC24)

  28. Where is it? Mitochondrial p450 mitochondrial inner membrane GO cellular component term: GO:0005743

  29. What does it do? substrate + O2 = CO2 +H20 product monooxygenase activity GO molecular function term: GO:0004497

  30. Which process is this? electron transport GO biological process term: GO:0006118 http://ntri.tamuk.edu/cell/ mitochondrion/krebpic.html

  31. Molecular function ontology Nucleic acid binding is a type of binding. is_a is_a DNA binding is a type of nucleic acid binding.

  32. Biological process ontology Adaxial/abaxial pattern formation is a type of pattern specification. is_a is_a part_of Adaxial/abaxial pattern specification is a part of adaxial/abaxial pattern formation.

  33. Cellular component ontology nucleus is part of the intracellular domain is_a membrane- bound organelle is a type of organelle part_of

  34. Categorizing gene products is called ‘annotation’. function component process The gene product inner no outer is involved in adaxial/abaxial axis specification.

  35. function component process The gene product inner no outer has transcription factor activity.

  36. function component process The gene product inner no outer is active in the nucleus.

  37. is_a part_of Clark et al., 2005 A diagram of the whole system.

  38. Clark et al., 2005 Many species groups annotate. We see the research of one function across all species.

  39. The Gene Ontology is for all species and that means we have to *bridge* some language barriers.

  40. Same name, same thing? http://www.darknessandlight.co.uk/cambridge_photographs.html Bridge of Sighs, Cambridge. http://www.lockeheemstra.com/italy/bridge-of-sighs-venice.html Ponte dei Sospiri, Venice.

  41. Taction Tactition Tactile sense ? In biology…

  42. Taction Tactition Tactile sense perception of touch ; GO:0050975

  43. Bud initiation? An imaginary example.

  44. tooth bud initiation broad_synonym: bud initiation reproductive bud initiation broad_synonym: bud initiation shoot bud initiation broad_synonym: bud initiation

  45. Categorization of gene products using GO is called annotation. So how does that happen?

  46. P05147 Choose your favourite gene.

  47. P05147 PMID: 2976880 Find a paper about it.

  48. P05147 PMID: 2976880 GO:0047519 Find the GO term describing its function, process or location of action.

  49. P05147 PMID: 2976880 IDA What evidence do they show? GO:0047519

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