STRING - Modeling of biological systems through cross-species data integration

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12th European Congress on Biotechnology, Technical University of Denmark, Lyngby, Denmark, August 21-24, 2005

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STRING - Modeling of biological systems through cross-species data integration

  1. 1. STRING Modeling of biological systems through cross-species data integration Lars Juhl Jensen EMBL Heidelberg
  2. 2. Jensen et al., Drug Discovery Today: Targets, 2004
  3. 3. de Lichtenberg et al., Science, 2005
  4. 4. TOM MRPL Ribosome Related MRPS Vacuolar Acidification Fatty Acid Biosynth. Secondary RCC_Asy RCC_Asy RCCII RCCIV RCCV RCC_Asy HAP Complex Arg Biosynth. PDH/KGD/ GCV Cell Wall & pH Reg. DNA Repair Glucose sensing and CH remodelling APC Fission/ Fusion rRNA Processing mRNA Processing TFIIIC Complex m-AAA Complex TCA Cycle Iron Homeostasis/ Chaperone Activity RCCI rRNA Processing Leu/Val/Ile Biosynth. DNA Repair GARP Complex Cytosolic Ribosome TIM RCC_Asy Actin tRNA Splicing RCCIII NUP Replication/ DNA Repair
  5. 5. TOM MRPL Ribosome Related MRPS Vacuolar Acidification Fatty Acid Biosynth. Secondary RCC_Asy RCC_Asy RCCII RCCIV RCCV RCC_Asy HAP Complex Arg Biosynth. PDH/KGD/ GCV Cell Wall & pH Reg. DNA Repair Glucose sensing and CH remodelling APC Fission/ Fusion rRNA Processing mRNA Processing TFIIIC Complex m-AAA Complex TCA Cycle Iron Homeostasis/ Chaperone Activity RCCI rRNA Processing Leu/Val/Ile Biosynth. DNA Repair GARP Complex Cytosolic Ribosome TIM RCC_Asy Actin tRNA Splicing RCCIII NUP Replication/ DNA Repair Protobacterial orthologs
  6. 6. TOM MRPL Ribosome Related MRPS Vacuolar Acidification Fatty Acid Biosynth. Secondary RCC_Asy RCCII RCCIV RCCV RCC_Asy HAP Complex Arg Biosynth. PDH/KGD/ GCV Cell Wall & pH Reg. DNA Repair Glucose sensing and CH remodelling APC Fission/ Fusion rRNA Processing mRNA Processing TFIIIC Complex m-AAA Complex TCA Cycle Iron Homeostasis/ Chaperone Activity RCCI rRNA Processing Leu/Val/Ile Biosynth. DNA Repair GARP Complex Cytosolic Ribosome TIM RCC_Asy Actin tRNA Splicing RCCIII NUP Replication/ DNA Repair Human disease orthologs RCC_Asy
  7. 7. Genomic neighborhood Species co-occurrence Gene fusions Database imports Exp. interaction data Microarray expression data Literature co-mentioning von Mering et al., Nucleic Acids Res., 2005
  8. 8. T Resting protuberances Protracted protuberance Cellulose © Trends Microbiol, 1999 Cell Cell wall Anchoring proteins Cellulosomes Cellulose The “Cellulosome”
  9. 10. Jensen et al., to appear in Nat. Rev. Genet., 2005
  10. 11. Networ-Kin™ Phospho-peptide data (from MS) Predict the kinase class (NetPhosK and Scansite)
  11. 12. Summary <ul><li>Quality control is crucial for large-scale data integration </li></ul><ul><ul><li>The raw data sets from high-throughput experiments are dirty </li></ul></ul><ul><ul><li>Scoring, benchmarking, and filtering can greatly improve the quality </li></ul></ul><ul><li>Data integration should be done across multiple species </li></ul><ul><li>Automated literature mining methods are (finally) maturing </li></ul><ul><ul><li>Restricted types of information can be extracted with high precision </li></ul></ul><ul><ul><li>Text mining methods can lead to novel discoveries </li></ul></ul><ul><li>Protein networks are more than just pretty pictures </li></ul><ul><ul><li>Highly specific hypotheses can be made from high-quality networks </li></ul></ul>
  12. 13. 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>Sean Hooper </li></ul></ul><ul><ul><li>Mathilde Foglierini </li></ul></ul><ul><ul><li>Julien Lagarde </li></ul></ul><ul><ul><li>Peer Bork </li></ul></ul><ul><li>Text mining project </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><ul><li>Networ-Kin </li></ul><ul><ul><li>Rune Linding </li></ul></ul><ul><ul><li>Tony Pawson </li></ul></ul><ul><li>Analysis of yeast mitochondria </li></ul><ul><ul><li>Fabiana Perocchi </li></ul></ul><ul><ul><li>Lars Steinmetz </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>
  13. 14. Thank you!

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