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Information integration
 

Information integration

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    Information integration Information integration Presentation Transcript

    • Information integration Lars Juhl Jensen
    • Part 1the eukaryotic cell cycle
    • essential process
    • grow and divide
    • one cell
    • two cells
    • four phases
    • G1 phase
    • growth
    • S phase
    • DNA replication
    • G2 phase
    • growth
    • M phase
    • cell division
    • regulation
    • gene expression
    • phosphorylation
    • targeted degradation
    • protein interactions
    • Example 1my protein and friends
    • http://string-db.org
    • Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
    • Part 2association networks
    • guild by association
    • STRING
    • >1100 genomes
    • genomic context
    • gene fusion
    • Korbel et al., Nature Biotechnology, 2004
    • conserved neighborhood
    • Korbel et al., Nature Biotechnology, 2004
    • phylogenetic profiles
    • Korbel et al., Nature Biotechnology, 2004
    • protein interactions
    • Jensen & Bork, Science, 2008
    • genetic interactions
    • Beyer et al., Nature Reviews Genetics, 2007
    • gene coexpression
    • curated knowledge
    • Letunic & Bork, Trends in Biochemical Sciences, 2008
    • >10 km
    • text mining
    • co-mentioning
    • NLPNatural Language Processing
    • Gene and protein namesCue words for entity recognitionVerbs for relation extraction[nxgene The GAL4 gene][nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]] is controlled by [nxpg HAP1]
    • different sources
    • different formats
    • different names
    • not comparable
    • variable quality
    • many parsers
    • comprehensive lexicon
    • quality scores
    • look at the data
    • von Mering et al., Nucleic Acids Research, 2005
    • scoring scheme
    • benchmark
    • von Mering et al., Nucleic Acids Research, 2005
    • probabilistic scores
    • combine scores
    • Example 2evidence filters and viewers
    • highest confidence only
    • experiments only
    • evidence viewers
    • Part 3analysis of cell-cycle data
    • gene expression
    • cell cultures
    • synchronization
    • microarrays
    • time courses
    • look at the data
    • Gauthier et al., Nucleic Acids Research, 2007
    • scoring scheme
    • benchmark
    • time of peak expression
    • protein interactions
    • temporal network
    • de Lichtenberg, Jensen et al., Science, 2005
    • Example 3a network for my proteins
    • http://string-db.org
    • high confidence only
    • experiments only
    • network expansion
    • Part 4external data
    • save network
    • open in Cytoscape
    • layout
    • clustering
    • project data onto network
    • de Lichtenberg, Jensen et al., Science, 2005
    • very flexible
    • lose the STRING interface
    • payload mechanism
    • show external data
    • nodes
    • edges
    • hosted on your server
    • Example 4my data in STRING
    • http://cyclebase-string.jensenlab.org
    • Conclusions
    • know your question
    • collect data
    • look at the data
    • benchmark
    • Thank you!
    • larsjuhljensen