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Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
Data integration and functional association networks
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Data integration and functional association networks

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Exploring Modular Protein Architecture, European Molecular Biology Laboratory, Heidelberg, Germany, December 3-5, 2008

Exploring Modular Protein Architecture, European Molecular Biology Laboratory, Heidelberg, Germany, December 3-5, 2008

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  • 1. Lars Juhl Jensen Data integration and functional association networks
  • 2. Lars Juhl Jensen Data integration and functional association networks
  • 3. if this is your plan
  • 4.  
  • 5.  
  • 6. STRING
  • 7. Jensen, Kuhn et al., Nucleic Acids Research , 2009
  • 8. data integration
  • 9. functional associations
  • 10. Frishman et al., Modern Genome Annotation , 2009
  • 11. the basis
  • 12. 630 genomes
  • 13. model organism databases
  • 14. Ensembl
  • 15. RefSeq
  • 16. genomic context methods
  • 17. gene fusion
  • 18. Korbel et al., Nature Biotechnology , 2004
  • 19. conserved neighborhood
  • 20. Korbel et al., Nature Biotechnology , 2004
  • 21. phylogenetic profiles
  • 22. Korbel et al., Nature Biotechnology , 2004
  • 23. primary experimental data
  • 24. gene coexpression
  • 25.  
  • 26. GEO Gene Expression Omnibus
  • 27. protein interactions
  • 28. Jensen & Bork, Science , 2008
  • 29. BIND Biomolecular Interaction Network Database
  • 30. BioGRID General Repository for Interaction Datasets
  • 31. DIP Database of Interacting Proteins
  • 32. IntAct
  • 33. MINT Molecular Interactions Database
  • 34. HPRD Human Protein Reference Database
  • 35. PDB Protein Data Bank
  • 36. curated knowledge
  • 37. complexes
  • 38. MIPS Munich Information center for Protein Sequences
  • 39. Gene Ontology
  • 40. pathways
  • 41. Letunic & Bork, Trends in Biochemical Sciences , 2008
  • 42. KEGG Kyoto Encyclopedia of Genes and Genomes
  • 43. MetaCyc
  • 44. Reactome
  • 45. PID NCI-Nature Pathway Interaction Database
  • 46. literature mining
  • 47. M EDLINE
  • 48. SGD Saccharomyces Genome Database
  • 49. The Interactive Fly
  • 50. OMIM Online Mendelian Inheritance in Man
  • 51. thesaurus
  • 52. co-mentioning
  • 53.  
  • 54. NLP Natural Language Processing
  • 55. <ul><li>Gene and protein names </li></ul><ul><li>Cue words for entity recognition </li></ul><ul><li>Verbs for relation extraction </li></ul><ul><li>[ nxgene The GAL4 gene ] </li></ul><ul><li>[ nxexpr T he expression of [ nxgene the cytochrome genes [ nxpg CYC1 and CYC7 ]]] is controlled by [ nxpg HAP1 ] </li></ul>
  • 56. too easy …
  • 57. … to be true
  • 58. many data types
  • 59. not comparable
  • 60. different error rates
  • 61. many sources
  • 62. different file formats
  • 63. different gene identifiers
  • 64. redundancy
  • 65. spread over 630 genomes
  • 66. raw quality scores
  • 67. reproducibility
  • 68. von Mering et al., Nucleic Acids Research , 2005
  • 69. intergenic distances
  • 70. Korbel et al., Nature Biotechnology , 2004
  • 71. benchmarking
  • 72. calibrate vs. gold standard
  • 73. von Mering et al., Nucleic Acids Research , 2005
  • 74. raw quality scores
  • 75. probabilistic scores
  • 76. transfer by orthology
  • 77. von Mering et al., Nucleic Acids Research , 2005
  • 78. two modes
  • 79. COG mode
  • 80. von Mering et al., Nucleic Acids Research , 2005
  • 81. protein mode
  • 82. von Mering et al., Nucleic Acids Research , 2005
  • 83. combine all evidence
  • 84. visualize
  • 85. Frishman et al., Modern Genome Annotation , 2009
  • 86. related resources
  • 87. STITCH
  • 88. &nbsp;
  • 89. protein–chemical network
  • 90. &nbsp;
  • 91. Reflect
  • 92. &nbsp;
  • 93. eggNOG
  • 94. orthologous groups
  • 95. &nbsp;
  • 96. NetworKIN
  • 97. &nbsp;
  • 98. Linding, Jensen, Ostheimer et al., Cell , 2007
  • 99. Acknowledgments <ul><li>NetworKIN.info </li></ul><ul><ul><li>Rune Linding </li></ul></ul><ul><ul><li>Gerard Ostheimer </li></ul></ul><ul><ul><li>Francesca Diella </li></ul></ul><ul><ul><li>Karen Colwill </li></ul></ul><ul><ul><li>Jing Jin </li></ul></ul><ul><ul><li>Pavel Metalnikov </li></ul></ul><ul><ul><li>Vivian Nguyen </li></ul></ul><ul><ul><li>Adrian Pasculescu </li></ul></ul><ul><ul><li>Jin Gyoon Park </li></ul></ul><ul><ul><li>Leona D. Samson </li></ul></ul><ul><ul><li>Rob Russell </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><ul><li>Michael Yaffe </li></ul></ul><ul><ul><li>Tony Pawson </li></ul></ul><ul><li>STRING.embl.de </li></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Manuel Stark </li></ul></ul><ul><ul><li>Samuel Chaffron </li></ul></ul><ul><ul><li>Chris Creevey </li></ul></ul><ul><ul><li>Jean Muller </li></ul></ul><ul><ul><li>Tobias Doerks </li></ul></ul><ul><ul><li>Philippe Julien </li></ul></ul><ul><ul><li>Alexander Roth </li></ul></ul><ul><ul><li>Milan Simonovic </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><ul><li>Christian von Mering </li></ul></ul><ul><li>STITCH.embl.de </li></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Christian von Mering </li></ul></ul><ul><ul><li>Monica Campillos </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><li>eggNOG.embl.de </li></ul><ul><ul><li>Philippe Julien </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Christian von Mering </li></ul></ul><ul><ul><li>Jean Muller </li></ul></ul><ul><ul><li>Tobias Doerks </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><li>Reflect.ws </li></ul><ul><ul><li>Sean O’Donoghue </li></ul></ul><ul><ul><li>Evangelos Pafilis </li></ul></ul><ul><ul><li>Heiko Horn </li></ul></ul><ul><ul><li>Michael Kuhn </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><ul><li>Reinhardt Schneider </li></ul></ul>

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