Interaction prediction with STRING - Principles and examples

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

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  • Interaction prediction with STRING - Principles and examples

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

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