Protein interaction networks from yeast to human
Upcoming SlideShare
Loading in...5
×
 

Protein interaction networks from yeast to human

on

  • 1,140 views

Danish Proteomics Society and Danish Society for Biochemistry and Molecular Biology Symposium, University of Southern Denmark, Odense, Denmark, December 8, 2005

Danish Proteomics Society and Danish Society for Biochemistry and Molecular Biology Symposium, University of Southern Denmark, Odense, Denmark, December 8, 2005

Statistics

Views

Total Views
1,140
Views on SlideShare
1,139
Embed Views
1

Actions

Likes
0
Downloads
32
Comments
0

1 Embed 1

http://www.slideshare.net 1

Accessibility

Categories

Upload Details

Uploaded via as Microsoft PowerPoint

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

    Protein interaction networks from yeast to human Protein interaction networks from yeast to human Presentation Transcript

    • Protein interaction networks from yeast to human Lars Juhl Jensen EMBL Heidelberg
    • Current Opinion in Structural Biology, 2005
    • STRING
    •  
    • integrate diverse evidence
    • functional interactions
    • Bork et al., Current Opinion in Structural Biology, 2005
    • hundreds of proteomes
    • evolution
    •  
    •  
    • statistics
    • (the original sin)
    • prokaryotes
    • genomic context methods
    • gene fusion
    •  
    • gene neighborhood
    •  
    • phylogenetic profiles
    •  
    •  
    •  
    •  
    • Cell Cellulosomes Cellulose
    • eukaryotes
    • integrate diverse datasets
    • Jensen et al., Drug Discovery Today: Targets, 2004
    • curated knowledge
    • MIPS Munich Information center for Protein Sequences
    • KEGG Kyoto Encyclopedia of Genes and Genomes
    • STKE Signal Transduction Knowledge Environment
    • Reactome
    • literature mining
    • co-mentioning
    • NLP Natural Language Processing
    • M EDLINE
    • SGD Saccharomyces Genome Database
    • The Interactive Fly
    • OMIM Online Mendelian Inheritance in Man
    • primary experimental data
    • microarray expression data
    • GEO Gene Expression Omnibus
    • physical protein interactions
    • BIND Biomolecular Interaction Network Database
    • MINT Molecular Interactions Database
    • GRID General Repository for Interaction Datasets
    • DIP Database of Interacting Proteins
    • HPRD Human Protein Reference Database
    • problems
    • many sources
    • (different gene identifiers)
    • many types of evidence
    • questionable quality
    • not directly comparable
    • spread over many species
    • huge synonyms lists
    • calculate raw quality scores
    • calibrate vs. gold standard
    • KEGG Kyoto Encyclopedia of Genes and Genomes
    • von Mering et al., Nucleic Acids Research, 2005
    • transfer based on orthology
    • combine all evidence
    • Bork et al., Current Opinion in Structural Biology, 2005
    • Networ-Kin™ Phospho-peptide data (from MS) Predict the kinase class (NetPhosK and Scansite)
    • the human interactome
    • yeast two-hybrid
    • 1936 13 4 4 1385 65 18465 Stelzl et al. Rual et al. Small-scale studies
    • 32 0 3 4 18 4 23 Stelzl et al. Rual et al. Small-scale studies
    • 62 8 39 Small-scale studies Stelzl et al. Rual et al. 852 17 473 432 69 260
    • 3.5% and 21% sensitivity
    • in a couple of years
    • the human interactome
    • 100% = 1/5?
    • the yeast interactome
    • five years ago
    • yeast two-hybrid
    • 1150 117 117 72 4053 118 4469 Uetz et al. Ito et al. Small-scale studies
    • 162 53 34 72 180 29 338 Uetz et al. Ito et al. Small-scale studies
    • 511 189 616 Small-scale studies Uetz et al. Ito et al. 439 178 759 897 190 1347
    • 19% and 12% sensitivity
    • three years ago
    • complex purification and MS
    • 14186 784 1178 287 19492 230 3475 Gavin et al. Ho et al. Small-scale studies
    • 2341 125 656 287 2725 42 149 Gavin et al. Ho et al. Small-scale studies
    • 4431 1465 5041 Small-scale studies Gavin et al. Ho et al. 14913 1071 632 8047 517 746
    • 63% and 41% sensitivity
    • today
    • combining all available data
    • scoring and filtering
    •  
    • de Lichtenberg et al., Science, 2005
    • de Lichtenberg et al., Science, 2005
    • de Lichtenberg et al., Science, 2005
    • de Lichtenberg et al., Science, 2005
    • de Lichtenberg et al., Science, 2005
    • the challenge
    • how to get from here …
    • 1936 13 4 4 1385 65 18465 Stelzl et al. Rual et al. Small-scale studies
    • … to there …
    • de Lichtenberg et al., Science, 2005
    • yeast two-hybrid
    • complex purification and MS
    • scoring and filtering
    • Acknowledgments
      • The STRING team (EMBL)
        • Christian von Mering
        • Berend Snel
        • Martijn Huynen
        • Sean Hooper
        • Mathilde Foglierini
        • Julien Lagarde
        • Peer Bork
      • Literature mining project (EML Research)
        • Jasmin Saric
        • Rossitza Ouzounova
        • Isabel Rojas
      • Cell cycle studies (CBS)
        • Ulrik de Lichtenberg
        • Thomas Skøt Jensen
        • Søren Brunak
      • Networ-Kin™ (Mt. Sinai)
        • Rune Linding
        • Tony Pawson
      • Inspiration for presentation
        • Lawrence Lessig
        • Dick Clarence Hardt
        • Anders Gorm Pedersen
    • Thank you!