The STRING database

570 views

Published on

14th International Conference on Intelligent Systems for Molecular Biology, Software demo, Fortaleza Conference Center, Fortaleza, Brazil, August 6-10, 2006

Published in: Technology
  • Be the first to comment

  • Be the first to like this

The STRING database

  1. 1. The STRING database Lars Juhl Jensen EMBL Heidelberg
  2. 2. data integration
  3. 4. functional interactions
  4. 6. 179 proteomes
  5. 7. Ensembl
  6. 8. SWISS-PROT
  7. 9. genomic context methods
  8. 10. phylogenetic profiles
  9. 15. Cell Cellulosomes Cellulose
  10. 16. gene fusion
  11. 18. gene neighborhood
  12. 20. questionable reliability
  13. 21. raw quality scores
  14. 22. gene neighborhood
  15. 23. sum of intergenic distances
  16. 25. many types of evidence
  17. 26. raw quality scores
  18. 27. not directly comparable
  19. 28. benchmarking
  20. 29. calibrate against KEGG
  21. 31. curated knowledge
  22. 32. KEGG Kyoto Encyclopedia of Genes and Genomes
  23. 33. Reactome
  24. 34. MIPS Munich Information center for Protein Sequences
  25. 35. STKE Signal Transduction Knowledge Environment
  26. 36. primary experimental data
  27. 37. many sources
  28. 38. parsers
  29. 39. co-expression
  30. 40. GEO Gene Expression Omnibus
  31. 41. SMD Stanford Microarray Database
  32. 42. physical protein interactions
  33. 43. BIND Biomolecular Interaction Network Database
  34. 44. MINT Molecular Interactions Database
  35. 45. GRID General Repository for Interaction Datasets
  36. 46. DIP Database of Interacting Proteins
  37. 47. HPRD Human Protein Reference Database
  38. 48. literature mining
  39. 49. different gene identifiers
  40. 50. synonyms lists
  41. 51. M EDLINE
  42. 52. SGD Saccharomyces Genome Database
  43. 53. The Interactive Fly
  44. 54. OMIM Online Mendelian Inheritance in Man
  45. 55. co-mentioning
  46. 56. NLP Natural Language Processing
  47. 57. <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>
  48. 59. combine all evidence
  49. 60. spread over many species
  50. 61. transfer by orthology
  51. 63. orthologous groups
  52. 65. fuzzy orthology
  53. 66. ? Source species Target species
  54. 67. Bayesian scoring scheme
  55. 69. Acknowledgments <ul><li>The STRING team (EMBL) </li></ul><ul><ul><li>Christian von Mering </li></ul></ul><ul><ul><li>Berend Snel </li></ul></ul><ul><ul><li>Martijn Huynen </li></ul></ul><ul><ul><li>Sean Hooper </li></ul></ul><ul><ul><li>Samuel Chaffron </li></ul></ul><ul><ul><li>Julien Lagarde </li></ul></ul><ul><ul><li>Mathilde Foglierini </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><li>Literature mining project (EML Research) </li></ul><ul><ul><li>Jasmin Saric </li></ul></ul><ul><ul><li>Rossitza Ouzounova </li></ul></ul><ul><ul><li>Isabel Rojas </li></ul></ul>

×