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Standards in Alternative Splicing
 

Standards in Alternative Splicing

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Presentation given at ISMB AltSplice Sig 2006

Presentation given at ISMB AltSplice Sig 2006

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    Standards in Alternative Splicing Standards in Alternative Splicing Presentation Transcript

    • Standards in Alternative Splicing AS-SIG 2006, Fortaleza, Brazil Oliver Hofmann South African National Bioinformatics Institute
    • Data integration Expression source Splicing event Transcription regulation
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    • Expression source Splicing event Transcription regulation
    • eVOC system
      • hierarchical, controlled vocabulary
      • Anatomical system
      • Cell type
      • Developmental stage
      • Pathology
    • eVOC system
      • hierarchical, controlled vocabulary
      • Anatomical system
      • Cell type
      • Developmental stage
      • Pathology
    •  
    •  
    • 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
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    • Differential TSS
    • Expression source Splicing event Transcription regulation
    • Requirements
      • Vocabulary
      • Definitions
      • (Data Model)
      • Encoding
    • Vocabulary
      • Donor site
      5'-splice site
    • Vocabulary
      • Donor site
      • Cassette exon
      5'-splice site Skipped exon
    • Vocabulary
      • Donor site
      • Cassette exon
      • Retained intron
      5'-splice site Skipped exon Cryptic exon
    • Definitions
      • „ Cassette exons are exons that are seen in some transcripts, and not in others.“
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      • Cassette exon
      Cryptic exon Skipped exon Normal form?
      • Genome
      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
      • „ Cassette exons are exons that are seen in some transcripts, and not in others.“
    • Definitions revisited
      • (I <is an> SO:INTRON
      • and (E <is an> SO:EXON)
      • and (E <is contained in> I)
      A D A D
    • Searching for subgraphs
      • Modified acceptor site
      A A D D
    •  
    • Rules and graphs
      • Can be concatenated to more complex rules
      • Definitions can be translated as required
    • Encoding
      • tromer
      SpliceNest ECGene Alternative Splicing Gallery Alternate Transcript Diversity
    • 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/
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    • Expression source Splicing event Transcription regulation
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    • Thank you!
      • Christian Iseli
      • Chris Mungall
      Michael Sammeth Eduardo Eyras
    • http://www.sanbi.ac.za/ Standards in Alternative Splicing Encoding Alternative Splicing Information