Data integration and functional association networks

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

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Data integration and functional association networks

  1. 1. Lars Juhl Jensen Data integration and functional association networks
  2. 2. Lars Juhl Jensen Data integration and functional association networks
  3. 3. if this is your plan
  4. 6. STRING
  5. 7. Jensen, Kuhn et al., Nucleic Acids Research , 2009
  6. 8. data integration
  7. 9. functional associations
  8. 10. Frishman et al., Modern Genome Annotation , 2009
  9. 11. the basis
  10. 12. 630 genomes
  11. 13. model organism databases
  12. 14. Ensembl
  13. 15. RefSeq
  14. 16. genomic context methods
  15. 17. gene fusion
  16. 18. Korbel et al., Nature Biotechnology , 2004
  17. 19. conserved neighborhood
  18. 20. Korbel et al., Nature Biotechnology , 2004
  19. 21. phylogenetic profiles
  20. 22. Korbel et al., Nature Biotechnology , 2004
  21. 23. primary experimental data
  22. 24. gene coexpression
  23. 26. GEO Gene Expression Omnibus
  24. 27. protein interactions
  25. 28. Jensen & Bork, Science , 2008
  26. 29. BIND Biomolecular Interaction Network Database
  27. 30. BioGRID General Repository for Interaction Datasets
  28. 31. DIP Database of Interacting Proteins
  29. 32. IntAct
  30. 33. MINT Molecular Interactions Database
  31. 34. HPRD Human Protein Reference Database
  32. 35. PDB Protein Data Bank
  33. 36. curated knowledge
  34. 37. complexes
  35. 38. MIPS Munich Information center for Protein Sequences
  36. 39. Gene Ontology
  37. 40. pathways
  38. 41. Letunic & Bork, Trends in Biochemical Sciences , 2008
  39. 42. KEGG Kyoto Encyclopedia of Genes and Genomes
  40. 43. MetaCyc
  41. 44. Reactome
  42. 45. PID NCI-Nature Pathway Interaction Database
  43. 46. literature mining
  44. 47. M EDLINE
  45. 48. SGD Saccharomyces Genome Database
  46. 49. The Interactive Fly
  47. 50. OMIM Online Mendelian Inheritance in Man
  48. 51. thesaurus
  49. 52. co-mentioning
  50. 54. NLP Natural Language Processing
  51. 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>
  52. 56. too easy …
  53. 57. … to be true
  54. 58. many data types
  55. 59. not comparable
  56. 60. different error rates
  57. 61. many sources
  58. 62. different file formats
  59. 63. different gene identifiers
  60. 64. redundancy
  61. 65. spread over 630 genomes
  62. 66. raw quality scores
  63. 67. reproducibility
  64. 68. von Mering et al., Nucleic Acids Research , 2005
  65. 69. intergenic distances
  66. 70. Korbel et al., Nature Biotechnology , 2004
  67. 71. benchmarking
  68. 72. calibrate vs. gold standard
  69. 73. von Mering et al., Nucleic Acids Research , 2005
  70. 74. raw quality scores
  71. 75. probabilistic scores
  72. 76. transfer by orthology
  73. 77. von Mering et al., Nucleic Acids Research , 2005
  74. 78. two modes
  75. 79. COG mode
  76. 80. von Mering et al., Nucleic Acids Research , 2005
  77. 81. protein mode
  78. 82. von Mering et al., Nucleic Acids Research , 2005
  79. 83. combine all evidence
  80. 84. visualize
  81. 85. Frishman et al., Modern Genome Annotation , 2009
  82. 86. related resources
  83. 87. STITCH
  84. 89. protein–chemical network
  85. 91. Reflect
  86. 93. eggNOG
  87. 94. orthologous groups
  88. 96. NetworKIN
  89. 98. Linding, Jensen, Ostheimer et al., Cell , 2007
  90. 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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