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Network biology: Large-scale biomedical data and text mining
 

Network biology: Large-scale biomedical data and text mining

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Network biology: Large-scale biomedical data and text mining Network biology: Large-scale biomedical data and text mining Presentation Transcript

  • Network biology Large-scale biomedical data and text mining Lars Juhl Jensen
  • three parts
  • association networks
  • signaling networks
  • drug networks
  • Part 1 association networks
  • guilt by association
  •  
  • STRING
  • Szklarczyk, Franceschini et al., Nucleic Acids Research , 2011
  • >1100 genomes
  • genomic context
  • gene fusion
  • Korbel et al., Nature Biotechnology , 2004
  • experimental data
  • protein interactions
  • Jensen & Bork, Science , 2008
  • curated knowledge
  • pathways
  • Letunic & Bork, Trends in Biochemical Sciences , 2008
  • many data types
  • many databases
  • different formats
  • different identifiers
  • variable quality
  • quality scores
  • von Mering et al., Nucleic Acids Research , 2005
  • calibrate vs. gold standard
  • von Mering et al., Nucleic Acids Research , 2005
  • orthology transfer
  • missing most of the data
  • >10 km
  • too much to read
  • computer
  • as smart as a dog
  • teach it specific tricks
  •  
  •  
  • named entity recognition
  • identify the concepts
  • proteins
  • comprehensive lexicon
  • orthographic variation
  • “ black list”
  • Reflect
  • augmented browsing
  • Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009 O’Donoghue et al., Journal of Web Semantics , 2010
  • information extraction
  • co-mentioning
  •  
  • Part 2 signaling networks
  • phosphoproteomics
  • in vivo phosphosites
  • kinases are unknown
  • sequence specificity
  • Miller, Jensen et al., Science Signaling , 2008
  • NetPhorest
  • automated pipeline
  • Miller, Jensen et al., Science Signaling , 2008
  • protein-specific
  • no context
  • co-activators
  • protein scaffolds
  • localization
  • expression
  • association network
  • Linding, Jensen, Ostheimer et al., Cell , 2007
  • NetworKIN
  • Linding, Jensen, Ostheimer et al., Cell , 2007
  •  
  • Part 3 drug networks
  • drug repurposing
  • drug–drug network
  • chemical similarity
  • Campillos & Kuhn et al., Science , 2008
  • only trivial predictions
  • phenotypic similarity
  • chemical perturbations
  • phenotypic readouts
  • drug treatment
  • side effects
  • no database
  • package inserts
  • Campillos & Kuhn et al., Science , 2008
  • text mining
  • manual validation
  • SIDER
  • side-effect similarity
  • Campillos & Kuhn et al., Science , 2008
  • combined similarity
  • Campillos & Kuhn et al., Science , 2008
  • categorization
  • Campillos & Kuhn et al., Science , 2008
  • 20 drug–drug pairs
  • in vitro binding assays
  • K i <10 µM for 11 of 20
  • cell assays
  • 9 of 9 showed activity
  • Acknowledgments
      • Reflect
      • Sune Frankild
      • Heiko Horn
      • Evangelos Pafilis
      • Michael Kuhn
      • Reinhardt Schneider
      • Sean O’Donoghue
      • Side effects
      • Monica Campillos
      • Michael Kuhn
      • Anne-Claude Gavin
      • Peer Bork
      • STRING
      • Damian Szklarczyk
      • Andrea Franceschini
      • Michael Kuhn
      • Milan Simonovic
      • Alexander Roth
      • Pablo Minguez
      • Tobias Doerks
      • Manuel Stark
      • Jean Muller
      • Peer Bork
      • Christian von Mering
      • NetworKIN
      • Heiko Horn
      • Martin Lee Miller
      • Gerard Ostheimer
      • Francesca Diella
      • Claus Jørgensen
      • Rob Russell
      • Peer Bork
      • Benjamin Turk
      • Michael Yaffe
      • Tony Pawson
      • Rune Linding
  • larsjuhljensen