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Interaction prediction with STRING - Principles and examples
Interaction prediction with STRING - Principles and examples
Interaction prediction with STRING - Principles and examples
Interaction prediction with STRING - Principles and examples
Interaction prediction with STRING - Principles and examples
Interaction prediction with STRING - Principles and examples
Interaction prediction with STRING - Principles and examples
Interaction prediction with STRING - Principles and examples
Interaction prediction with STRING - Principles and examples
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Interaction prediction with STRING - Principles and examples

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EMBL Lab Day, European Molecular Biology Laboratory, Heidelberg, Germany, June 15, 2004

EMBL Lab Day, European Molecular Biology Laboratory, Heidelberg, Germany, June 15, 2004

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  • Transcript

    • 1. Interaction prediction with STRING Principles and examples Lars Juhl Jensen EMBL Heidelberg
    • 2. Too much information – too little knowledge
      • Biology is now in the age of large-scale data collection
        • Explosive increase in data from genome sequencing, microarray expression studies, screening for protein interactions etc.
        • The data types are highly heterogeneous
        • Much data is not being deposited in standardized repositories
        • Most data sets are error-prone and suffer from systematic biases
      • STRING is a web resource that integrates many different types of information across 100+ species
      • We do not intend STRING to be
        • a primary repository for experimental data
        • a curated database of complexes or pathways
        • a substitute for expert annotation
    • 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. Score calibration against a common reference
      • Many diverse types of evidence
        • The quality of each is judged by very different raw scores
        • These are all calibrated against the same reference set
      • Requirements for a reference
        • Must represent a compromise of the all types of evidence
        • Broad species coverage
      • Both a strength and a weakness
        • Scores for all evidence types are directly comparable
        • The type of interaction is currently not predicted
    • 7. Getting more specific – generally speaking
    • 8. Acknowledgments
      • The STRING team
        • Christian von Mering
        • Berend Snel
        • Martijn Huynen
        • Daniel Jaeggi
        • Steffen Schmidt
        • Mathilde Foglierini
        • Peer Bork
      • ArrayProspector web service
        • Julien Lagarde
        • Chris Workman
      • NetView visualization tool
        • Sean Hooper
      • Analysis of yeast cell cycle
        • Ulrik de Lichtenberg
        • Thomas Skøt
        • Anders Fausbøll
        • Søren Brunak
      • Web resources
        • http://string.embl.de
        • http://www.bork.embl.de/ ArrayProspector
        • http://www.bork.embl.de/ synonyms
    • 9. Thank you!

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