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The Gene Ontology Project

The Gene Ontology Project. An Introduction. There is a lot of biological research output. Search on mesoderm development…. You get 6752 results! How will you ever find what you want?. Another example…. time. control. attacked. Microarray data shows changed expression of

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The Gene Ontology Project

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  1. The Gene Ontology Project An Introduction

  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 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 every week. http://www.teamtechnology.co.uk/f-scientist.jpg http://www.kilbot.com.au/wp-content/shop/careful-scientist.gif

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

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

  12. Ontology is a way to capture knowledge in a written and computable form. Computable Computable means that the computer finds patterns so we don’t have to.

  13. Ebay search (keyword ‘lead’) v. Pubmed search (keyword ‘flower’) Demo and practical work

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

  20. time control attacked Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.

  21. See which processes are upregulated or downregulated. 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 Bregje Wertheim at the Centre for Evolutionary Genomics, Department of Biology, UCL and Eugene Schuster Group, EBI.

  22. Practical work: Search AmiGO Did you find your favourite gene product or process?

  23. How does the Gene Ontology work?

  24. 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.

  25. is_a part_of The whole system. Clark et al., 2005

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

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

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

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

  30. is_a part_of The whole system. Clark et al., 2005

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

  32. 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.

  33. Taction Tactition Tactile sense ? In biology…

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

  35. Bud initiation?

  36. = tooth bud initiation = reproductive bud initiation = branch bud initiation

  37. Demo: Writing an ontology The car ontology

  38. Demo: The gene ontology

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

  40. P05147 Choose your favourite gene.

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

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

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

  44. P05147 GO:0047519 P05147 GO:0047519 IDA PMID:2976880 PMID: 2976880 IDA Write these down…

  45. . Send to the GO Consortium

  46. Finding annotations in a paper …for B. napus PERK1 protein (Q9ARH1) In this study, we report the isolation and molecular characterization of the B. napus PERK1 cDNA, that is predicted to encode a novel receptor-like kinase. We have shown that like other plant RLKs, the kinase domain of PERK1 has serine/threonine kinase activity, In addition, the location of a PERK1-GTP fusion protein to the plasma membrane supports the prediction that PERK1 is an integral membrane protein…these kinases have been implicated in early stages of wound response… serine/threonine kinase activity, integral membrane protein wound response PubMed ID: 12374299 Function: protein serine/threonine kinase activity GO:0004674 Component: integral to plasma membrane GO:0005887 Process: response to wounding GO:0009611

  47. Annotation details

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