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Standards in Alternative Splicing AS-SIG 2006, Fortaleza, Brazil Oliver Hofmann South African National Bioinformatics Institute
Data integration Expression source Splicing  event Transcription regulation
 
 
 
Expression source Splicing  event Transcription regulation
eVOC system ,[object Object],[object Object],[object Object],[object Object],[object Object]
eVOC system ,[object Object],[object Object],[object Object],[object Object],[object Object]
 
 
eVOC mappings H-Inv Clusters UniGene GenBank cDNA libraries eVOC Gene ESTs RefSeq cDNA H-Inv cDNA
Fantom3 TU: 79236 GenBank Accessions Mouse RefSeq NM_054054 Human RefSeq (BRDT) MGI data Library annotation Human eVOC Homolog
Fantom3 TU: 79236 GenBank Accessions Mouse RefSeq NM_054054 Human RefSeq (BRDT) MGI data Library annotation Human eVOC Homolog
Expression source Splicing  event Transcription regulation
 
 
 
 
Differential TSS
Expression source Splicing  event Transcription regulation
Requirements ,[object Object],[object Object],[object Object],[object Object]
Vocabulary ,[object Object],5'-splice site
Vocabulary ,[object Object],[object Object],5'-splice site Skipped exon
Vocabulary ,[object Object],[object Object],[object Object],5'-splice site Skipped exon Cryptic exon
Definitions ,[object Object]
 
 
[object Object],Cryptic exon Skipped exon Normal form?
[object Object],T1 T2 T3
Sequence Ontology
Object description SO:Intron SO:5' splice site SO:Exon SO:3' splice site SO:Exon SO:Exon SO:Intron
Basic events
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
Pairwise description Exon 0 Exon 2 Exon 0 Exon 1 Exon 2 cassette exon
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
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
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
H 0 D 0 A 2 D 2 A 4 D 4 A 5 T 0 T 1 D 3 A 1 D 1
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
D 0 A 2 D 2 A 4 D 4 A 5 T 0 T 1 D 3 A 1 D 1
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
Definitions revisited ,[object Object]
Definitions revisited ,[object Object],[object Object],[object Object],A D A D
Searching for subgraphs ,[object Object],A A D D
 
Rules and graphs ,[object Object],[object Object]
Encoding ,[object Object],SpliceNest ECGene Alternative Splicing Gallery Alternate Transcript Diversity
SO & CHAOS-XML ,[object Object],[object Object]
 
Expression source Splicing  event Transcription regulation
 
Thank you! ,[object Object],[object Object],Michael Sammeth Eduardo Eyras
http://www.sanbi.ac.za/ Standards in Alternative Splicing Encoding Alternative Splicing Information

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Standards in Alternative Splicing