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

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Lars Juhl Jensen
Lars Juhl Jensen

Journée Thematique Biologie des Systèmes, INRA, Jouy-en-Josas, France, February 2, 2006

Technologie
1 von 100
STRING Modeling of biological systems through cross-species data integration
Lars Juhl Jensen
 
 
promoter analysis
Jensen et al., Bioinformatics, 2000
genome visualization
Pedersen et al., Journal of Molecular Biology, 2000
protein function prediction
 
 
 
STRING
 
integrate diverse evidence
functional interactions
Bork et al., Current Opinion in Structural Biology, 2005
179 proteomes
genomic context methods
phylogenetic profiles
 
 
 
 
Cell Cellulosomes Cellulose
anti-correlated profiles
 
analogous enzymes
Morett et al., Nature Biotechnology, 2003
gene neighborhood
 
bidirectional promoters
 
Korbel et al., Nature Biotechnology, 2004
gene fusion
 
evolution
 
 
statistics
(the original sin)
scoring and benchmarking
raw quality scores
gene neighborhood
sum of intergenic distances
 
many types of evidence
not directly comparable
calibrate vs. gold standard
 
curated knowledge
KEGG Kyoto Encyclopedia of Genes and Genomes
STKE Signal Transduction Knowledge Environment
Reactome
MIPS Munich Information center for Protein Sequences
primary experimental data
Jensen et al., Drug Discovery Today: Targets, 2004
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
von Mering et al., Nucleic Acids Research, 2005
literature mining
M EDLINE
SGD Saccharomyces Genome Database
The Interactive Fly
OMIM Online Mendelian Inheritance in Man
co-mentioning
different gene names
curated synonyms lists
NLP Natural Language Processing
[object Object],[object Object],[object Object],[object Object],[object Object]
Jensen et al., Nature Reviews Genetics, 2006
combine all evidence
na ïve Bayesian scheme
spread over many species
transfer based orthology
? Source species Target species
 
 
 
 
 
 
defining functional modules
 
 
qualitative modeling
the mitochondrial system
 
RCCs
predicting “mode of action”
Jensen et al., Drug Discovery Today: Targets, 2004
Jensen et al., Drug Discovery Today: Targets, 2004
Acknowledgments ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Thank you!

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