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