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Protein interaction networks
 

Protein interaction networks

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    Protein interaction networks Protein interaction networks Presentation Transcript

    • Protein interaction networks Lars Juhl Jensen
    • structure of interactions
    • physical networks
    • association networks
    • STRING
    • the cell cycle
    • essential process
    • grow and divide
    • one cell
    • two cells
    • four phases
    • G 1 phase
    • growth
    • S phase
    • DNA replication
    • G 2 phase
    • growth
    • M phase
    • cell division
    •  
    • regulation
    • gene expression
    • phosphorylation
    • targeted degradation
    • protein interactions
    • exercise 1
    • http://string-db.org
    • Szklarczyk, Franceschini et al., Nucleic Acids Research , 2011
    •  
    •  
    • association networks
    • guild by association
    •  
    • STRING
    • >1100 genomes
    • genomic context
    • gene fusion
    • Korbel et al., Nature Biotechnology , 2004
    • conserved neighborhood
    • Korbel et al., Nature Biotechnology , 2004
    • phylogenetic profiles
    • Korbel et al., Nature Biotechnology , 2004
    • protein interactions
    • Jensen & Bork, Science , 2008
    • genetic interactions
    • Beyer et al., Nature Reviews Genetics , 2007
    • gene coexpression
    •  
    • curated knowledge
    • Letunic & Bork, Trends in Biochemical Sciences , 2008
    • >10 km
    • text mining
    • Pafilis, O’Donoghue, Jensen et al., Nature Biotechnology , 2009
    • co-mentioning
    • NLP Natural Language Processing
    • different sources
    • Ensembl
    • RefSeq
    • BIND Biomolecular Interaction Network Database
    • BioGRID General Repository for Interaction Datasets
    • DIP Database of Interacting Proteins
    • IntAct
    • MINT Molecular Interactions Database
    • HPRD Human Protein Reference Database
    • PDB Protein Data Bank
    • GEO Gene Expression Omnibus
    • MIPS Munich Information center for Protein Sequences
    • Gene Ontology
    • BioCyc
    • KEGG Kyoto Encyclopedia of Genes and Genomes
    • PID NCI-Nature Pathway Interaction Database
    • Reactome
    • different formats
    • different names
    • CDC2
    • CDK1
    • P06493
    • not comparable
    • variable quality
    •  
    • confidence scores
    • von Mering et al., Nucleic Acids Research , 2005
    • transfer by orthology
    • von Mering et al., Nucleic Acids Research , 2005
    • combine scores
    • exercise 2
    • you are probably here
    •  
    •  
    • high confidence only
    •  
    • experiments only
    •  
    • evidence viewers
    •  
    • cell cycle analysis
    • gene expression
    • cell cultures
    • synchronization
    • microarrays
    •  
    • time courses
    • Gauthier et al., Nucleic Acids Research , 2007
    • cycling genes
    • time of peak expression
    •  
    • protein interactions
    • temporal network
    • de Lichtenberg, Jensen et al., Science , 2005
    • just-in-time assembly
    • de Lichtenberg, Jensen et al., Cell Cycle , 2007
    • evolutionary flexibility
    • orthologs and paralogs
    • protein complexes
    •  
    • exercise 3
    •  
    • http://string-db.org
    •  
    •  
    • network expansion
    •  
    •  
    • what is known
    •  
    • external data
    • save network
    •  
    • open in Cytoscape
    • layout
    • clustering
    • project data onto network
    • de Lichtenberg, Jensen et al., Science , 2005
    • very flexible
    • lose the STRING interface
    • payload mechanism
    • show external data
    • nodes
    • edges
    • hosted on your server
    • exercise 4
    •  
    • http://cyclebase-string.jensenlab.org
    •  
    •  
    • network expansion
    •  
    • CDK–cyclin complexes
    •  
    •  
    • chemical networks
    • STITCH
    • STRING + chemicals
    • PubChem compounds
    • >74,000 small molecules
    • experimental data
    • BindingDB
    • ChEMBL
    • PDSP K i Psycoactive Drug Screening Program
    • PDB Protein Data Bank
    • drug targets
    • CTD Comparative Toxicogenomics Database
    • DrugBank
    • GLIDA GPCR-Ligand Database
    • Matador
    • TTD Therapeutic Target Database
    • metabolic pathways
    • BioCyc
    • KEGG Kyoto Encyclopedia of Genes and Genomes
    • Reactome
    • exercise 5
    •  
    •  
    • http://stitch-db.org
    • Kuhn et al., Nucleic Acids Research , 2010
    •  
    •  
    • what is known
    •  
    • thank you!