Standards in Alternative Splicing

1,574
-1

Published on

Presentation given at ISMB AltSplice Sig 2006

Published in: Technology, Business
0 Comments
0 Likes
Statistics
Notes
  • Be the first to comment

  • Be the first to like this

No Downloads
Views
Total Views
1,574
On Slideshare
0
From Embeds
0
Number of Embeds
1
Actions
Shares
0
Downloads
0
Comments
0
Likes
0
Embeds 0
No embeds

No notes for slide

Standards in Alternative Splicing

  1. 1. Standards in Alternative Splicing AS-SIG 2006, Fortaleza, Brazil Oliver Hofmann South African National Bioinformatics Institute
  2. 2. Data integration Expression source Splicing event Transcription regulation
  3. 6. Expression source Splicing event Transcription regulation
  4. 7. eVOC system <ul><li>hierarchical, controlled vocabulary </li></ul><ul><li>Anatomical system </li></ul><ul><li>Cell type </li></ul><ul><li>Developmental stage </li></ul><ul><li>Pathology </li></ul>
  5. 8. eVOC system <ul><li>hierarchical, controlled vocabulary </li></ul><ul><li>Anatomical system </li></ul><ul><li>Cell type </li></ul><ul><li>Developmental stage </li></ul><ul><li>Pathology </li></ul>
  6. 11. eVOC mappings H-Inv Clusters UniGene GenBank cDNA libraries eVOC Gene ESTs RefSeq cDNA H-Inv cDNA
  7. 12. Fantom3 TU: 79236 GenBank Accessions Mouse RefSeq NM_054054 Human RefSeq (BRDT) MGI data Library annotation Human eVOC Homolog
  8. 13. Fantom3 TU: 79236 GenBank Accessions Mouse RefSeq NM_054054 Human RefSeq (BRDT) MGI data Library annotation Human eVOC Homolog
  9. 14. Expression source Splicing event Transcription regulation
  10. 19. Differential TSS
  11. 20. Expression source Splicing event Transcription regulation
  12. 21. Requirements <ul><li>Vocabulary </li></ul><ul><li>Definitions </li></ul><ul><li>(Data Model) </li></ul><ul><li>Encoding </li></ul>
  13. 22. Vocabulary <ul><li>Donor site </li></ul>5'-splice site
  14. 23. Vocabulary <ul><li>Donor site </li></ul><ul><li>Cassette exon </li></ul>5'-splice site Skipped exon
  15. 24. Vocabulary <ul><li>Donor site </li></ul><ul><li>Cassette exon </li></ul><ul><li>Retained intron </li></ul>5'-splice site Skipped exon Cryptic exon
  16. 25. Definitions <ul><li>„ Cassette exons are exons that are seen in some transcripts, and not in others.“ </li></ul>
  17. 28. <ul><li>Cassette exon </li></ul>Cryptic exon Skipped exon Normal form?
  18. 29. <ul><li>Genome </li></ul>T1 T2 T3
  19. 30. Sequence Ontology
  20. 31. Object description SO:Intron SO:5' splice site SO:Exon SO:3' splice site SO:Exon SO:Exon SO:Intron
  21. 32. Basic events
  22. 33. Pairwise description Exon 0 Exon 1 Exon 2 Exon 0 Exon 2 Exon 0 Exon 1 Exon 2 matches matches matches matches matches matches matches matches matches
  23. 34. Pairwise description Exon 0 Exon 2 Exon 0 Exon 1 Exon 2 cassette exon
  24. 35. Representation Exon 0 Exon 2 Exon 4 Exon 5 Exon 0 Exon 2 Exon 4 Exon 5 Exon 0 Exon 2 Exon 4 Exon 0 Exon 3 Exon 4 Exon 5 Exon 1
  25. 36. Exon 0 Exon 2 Exon 4 Exon 5 Exon 0 Exon 2 Exon 4 Exon 5 Exon 0 Exon 2 Exon 4 Exon 0 Exon 3 Exon 4 Exon 5 Exon 1 H 0 D 0 A 2 D 2 A 4 D 4 A 5 T 0 H 0 D 0 A 2 D 2 A 4 D 4 A 5 T 0 H 0 D 0 A 2 D 2 A 4 T 1 H 0 D 0 A 2 D 3 A 4 D 4 A 5 T 0 A 1 D 1
  26. 37. H 0 D 0 A 2 D 2 A 4 D 4 A 5 T 0 H 0 D 0 A 2 D 2 A 4 D 4 A 5 T 0 H 0 D 0 A 2 D 2 A 4 T 1 H 0 D 0 A 2 D 3 A 4 D 4 A 5 T 0 A 1 D 1
  27. 38. H 0 D 0 A 2 D 2 A 4 D 4 A 5 T 0 T 1 D 3 A 1 D 1
  28. 39. Edge information H 0 D 0 A 2 D 2 A 4 D 4 A 5 T 0 T 1 D 3 A 1 D 1
  29. 40. D 0 A 2 D 2 A 4 D 4 A 5 T 0 T 1 D 3 A 1 D 1
  30. 41. Colon cancer (6 ESTs) Normal Colon (20 ESTs) Heart (11 ESTs) H 0 D 0 A 2 D 2 A 4 D 4 A 5 T 0 T 1 D 3 A 1 D 1
  31. 42. Definitions revisited <ul><li>„ Cassette exons are exons that are seen in some transcripts, and not in others.“ </li></ul>
  32. 43. Definitions revisited <ul><li>(I <is an> SO:INTRON </li></ul><ul><li>and (E <is an> SO:EXON) </li></ul><ul><li>and (E <is contained in> I) </li></ul>A D A D
  33. 44. Searching for subgraphs <ul><li>Modified acceptor site </li></ul>A A D D
  34. 46. Rules and graphs <ul><li>Can be concatenated to more complex rules </li></ul><ul><li>Definitions can be translated as required </li></ul>
  35. 47. Encoding <ul><li>tromer </li></ul>SpliceNest ECGene Alternative Splicing Gallery Alternate Transcript Diversity
  36. 48. SO & CHAOS-XML <ul><li>„ Chaos-XML is for representing sequences and sequence features in a graph-like structure, typed according to SO.“ </li></ul><ul><li>http://www.fruitfly.org/chaos-xml/ </li></ul>
  37. 50. Expression source Splicing event Transcription regulation
  38. 52. Thank you! <ul><li>Christian Iseli </li></ul><ul><li>Chris Mungall </li></ul>Michael Sammeth Eduardo Eyras
  39. 53. http://www.sanbi.ac.za/ Standards in Alternative Splicing Encoding Alternative Splicing Information

×