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STRING - Predicting novel metabolic pathways through the integration of diverse genome-scale data
 

STRING - Predicting novel metabolic pathways through the integration of diverse genome-scale data

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12th International Conference on Intelligent Systems for Molecular Biology, BioPathways SIG, Scottish Exhibition & Conference Center, Glasgow, Scotland, July 29-August 4, 2004

12th International Conference on Intelligent Systems for Molecular Biology, BioPathways SIG, Scottish Exhibition & Conference Center, Glasgow, Scotland, July 29-August 4, 2004

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STRING - Predicting novel metabolic pathways through the integration of diverse genome-scale data STRING - Predicting novel metabolic pathways through the integration of diverse genome-scale data Presentation Transcript

  • STRING Predicting novel metabolic pathways through the integration of diverse genome-scale data Lars Juhl Jensen EMBL Heidelberg
  • 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
      • Objective definition of metabolic pathways / functional modules
      • Prediction of additional pathway members / novel pathways
    • 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
  • STRING provides a network of functional interactions between proteins Genomic neighborhood Species co-occurrence Gene fusions Database imports Exp. interaction data Microarray expression data 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”
  • 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
  • Multiple evidence types from several species
  • Objective definition of metabolic pathways Image: Molecular Biology of the Cell, 3 . rd edition Metabolism overview Defined manually: cutting metabolic maps into pathways Purine biosynthesis Histidine biosynthesis Defined objectively: standard clustering of genome-scale data
  • Getting more specific – generally speaking
  • 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
      • string.embl.de
      • www.bork.embl.de/ArrayProspector
      • www.bork.embl.de/synonyms
  • Thank you!