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Interaction prediction with STRING - Principles and examples

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Lars Juhl Jensen
Lars Juhl Jensen

STRING is a web resource that integrates diverse types of biological data like genomic neighborhood, gene fusions, and protein interactions across species to infer functional protein networks. It calibrates the different evidence types against a common reference set so that scores are directly comparable, even though the quality of each type is judged differently. The resource aims to provide a global view of known and predicted protein links to assist in functional predictions, but does not intend to replace specialized databases or expert annotation.

Technologie
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Interaction prediction with STRING Principles and examples Lars Juhl Jensen EMBL Heidelberg
Too much information – too little knowledge ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
STRING provides a protein network by integrating diverse types of evidence Genomic Neighborhood Species Co-occurrence Gene Fusions Database Imports Exp. Interaction Data Co-expression Literature Co-mentioning
Inferring functional modules from gene presence/absence patterns T rends in Microbiology Resting protuberances Protracted protuberance Cellulose © Trends Microbiol, 1999 Cell Cell wall Anchoring proteins Cellulosomes Cellulose The “Cellulosome”
Multiple evidence types from several species
Score calibration against a common reference ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Getting more specific – generally speaking
Acknowledgments ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Thank you!

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Interaction prediction with STRING - Principles and examples

  • 1. Interaction prediction with STRING Principles and examples Lars Juhl Jensen EMBL Heidelberg
  • 2.
  • 3. STRING provides a protein network by integrating diverse types of evidence Genomic Neighborhood Species Co-occurrence Gene Fusions Database Imports Exp. Interaction Data Co-expression Literature Co-mentioning
  • 4. Inferring functional modules from gene presence/absence patterns T rends in Microbiology Resting protuberances Protracted protuberance Cellulose © Trends Microbiol, 1999 Cell Cell wall Anchoring proteins Cellulosomes Cellulose The “Cellulosome”
  • 5. Multiple evidence types from several species
  • 6.
  • 7. Getting more specific – generally speaking
  • 8.