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Networks of proteins and diseases

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  • 1. Networks of proteins and diseases Lars Juhl Jensen
  • 2. three parts
  • 3. protein networks
  • 4. localization & disease
  • 5. disease networks
  • 6. protein networks
  • 7. Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011
  • 8. computational predictions
  • 9. gene fusion
  • 10. Korbel et al., Nature Biotechnology, 2004
  • 11. experimental data
  • 12. physical interactions
  • 13. Jensen & Bork, Science, 2008
  • 14. curated knowledge
  • 15. metabolic pathways
  • 16. Letunic & Bork, Trends in Biochemical Sciences, 2008
  • 17. text mining
  • 18. dictionary-based approach
  • 19. co-mentioning
  • 20. many databases
  • 21. different formats
  • 22. different identifiers
  • 23. variable quality
  • 24. not comparable
  • 25. hard work
  • 26. quality scores
  • 27. von Mering et al., Nucleic Acids Research, 2005
  • 28. calibrate vs. gold standard
  • 29. von Mering et al., Nucleic Acids Research, 2005
  • 30. localization & disease
  • 31. general approach
  • 32. suite of web resources
  • 33. curated knowledge
  • 34. experimental data
  • 35. text mining
  • 36. computational predictions
  • 37. quality scores
  • 38. data visualization
  • 39. compartments
  • 40. Gene Ontology
  • 41. compartments.jensenlab.org
  • 42. tissues
  • 43. BRENDA Tissue Ontology
  • 44. tissues.jensenlab.org
  • 45. diseases
  • 46. Disease Ontology
  • 47. removal of gene symbols
  • 48. addition of links
  • 49. evidence viewers
  • 50. web services
  • 51. diseases.jensenlab.org
  • 52. download files
  • 53. disease networks
  • 54. electronic health records
  • 55. Jensen et al., Nature Reviews Genetics, 2012
  • 56. structured data
  • 57. Jensen et al., Nature Reviews Genetics, 2012
  • 58. unstructured data
  • 59. comorbidity
  • 60. Jensen et al., Nature Reviews Genetics, 2012
  • 61. Roque et al., PLoS Computational Biology, 2011
  • 62. in Danish
  • 63. multiple testing
  • 64. confounding factors
  • 65. age and gender
  • 66. reporting bias
  • 67. molecular basis
  • 68. protein–disease links
  • 69. protein networks
  • 70. Acknowledgments STRING Christian von Mering Damian Szklarczyk Michael Kuhn Manuel Stark Samuel Chaffron Chris Creevey Jean Muller Tobias Doerks Philippe Julien Alexander Roth Milan Simonovic Jan Korbel Berend Snel Martijn Huynen Peer Bork Text mining Sune Frankild Evangelos Pafilis Alberto Santos Kalliopi Tsafou Janos Binder Lucia Fanini Sarah Faulwetter Christina Pavloudi Julia Schnetzer Aikaterini Vasileiadou Heiko Horn Michael Kuhn Nigel Brown Reinhard Schneider Sean O’Donoghue EHR mining Robert Eriksson Peter Bjødstrup Jensen Anders Boeck Jensen Francisco S. Roque Henriette Schmock Marlene Dalgaard Massimo Andreatta Thomas Hansen Karen Søeby Søren Bredkjær Anders Juul Tudor Oprea Pope Moseley Thomas Werge Søren Brunak

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