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Data integration - Integration of functional associations using STRING

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    Data integration - Integration of functional associations using STRING - Presentation Transcript

    1. Data integration Integration of functional associations using STRING Lars Juhl Jensen
    2. Jensen, Kuhn et al., Nucleic Acids Research , 2009
    3. functional associations
    4. confidence scores
    5. cross-species integration
    6. 630 genomes
    7. model organism databases
    8. Ensembl
    9. RefSeq
    10. defining orthology
    11. two modes
    12. protein mode
    13. von Mering et al., Nucleic Acids Research , 2005
    14. COG mode
    15. von Mering et al., Nucleic Acids Research , 2005
    16. genomic context
    17. gene fusion
    18. Korbel et al., Nature Biotechnology , 2004
    19. conserved neighborhood
    20. operons
    21. Korbel et al., Nature Biotechnology , 2004
    22. bidirectional promoters
    23. Korbel et al., Nature Biotechnology , 2004
    24. phylogenetic profiles
    25. Korbel et al., Nature Biotechnology , 2004
    26. examples
    27. bacterial Cox assembly
    28.  
    29. Banci et al., PNAS , 2005
    30. Banci et al., PNAS , 2005
    31. cellulose degradation
    32.  
    33.  
    34.  
    35. Cell Cellulosomes Cellulose
    36. experimental data
    37. protein interactions
    38. yeast two-hybrid
    39. affinity purification
    40. fragment complementation
    41. Jensen & Bork, Science , 2008
    42. genetic interactions
    43. Beyer et al., Nature Reviews Genetics , 2007
    44. BIND Biomolecular Interaction Network Database
    45. BioGRID General Repository for Interaction Datasets
    46. DIP Database of Interacting Proteins
    47. IntAct
    48. MINT Molecular Interactions Database
    49. HPRD Human Protein Reference Database
    50. PDB Protein Data Bank
    51. inferred associations
    52. gene coexpression
    53.  
    54. GEO Gene Expression Omnibus
    55. expression compendia
    56. curated knowledge
    57. complexes
    58. MIPS Munich Information center for Protein Sequences
    59. Gene Ontology
    60. pathways
    61. Letunic & Bork, Trends in Biochemical Sciences , 2008
    62. KEGG Kyoto Encyclopedia of Genes and Genomes
    63. MetaCyc
    64. Reactome
    65. PID NCI-Nature Pathway Interaction Database
    66. literature mining
    67. >10 km
    68. M EDLINE
    69. SGD Saccharomyces Genome Database
    70. The Interactive Fly
    71. OMIM Online Mendelian Inheritance in Man
    72. co-mentioning
    73. NLP Natural Language Processing
      • Gene and protein names
      • Cue words for entity recognition
      • Verbs for relation extraction
      • [ nxgene The GAL4 gene ]
      • [ nxexpr T he expression of [ nxgene the cytochrome genes [ nxpg CYC1 and CYC7 ]]] is controlled by [ nxpg HAP1 ]
    75.  
    76. easy in theory …
    77. … but not in practice
    78. many data types
    79. not comparable
    80. variable quality
    81. many sources
    82. different file formats
    83. different gene identifiers
    84. partially redundant
    85. spread over 630 genomes
    86. quality scores
    87. reproducibility
    88. von Mering et al., Nucleic Acids Research , 2005
    89. intergenic distances
    90.  
    91. benchmarking
    92. calibrate vs. gold standard
    93. von Mering et al., Nucleic Acids Research , 2005
    94. raw quality scores
    95. probabilistic scores
    96. integrate over orthologs
    97. protein mode
    98. von Mering et al., Nucleic Acids Research , 2005
    99. COG mode
    100. von Mering et al., Nucleic Acids Research , 2005
    101. combine all evidence
    102. Frishman et al., Modern Genome Annotation , 2009
    103. small molecules
    104. Kuhn et al., Nucleic Acids Research , 2008
    105. metametabolomics
    106. Acknowledgments
      • Christian von Mering
      • Michael Kuhn
      • Manuel Stark
      • Samuel Chaffron
      • Philippe Julien
      • Monica Campillos
      • Tobias Doerks
      • Jan Korbel
      • Berend Snel
      • Martijn Huynen
      • Peer Bork
    107. larsjuhljensen

    + Lars Juhl JensenLars Juhl Jensen, 1 month ago

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