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The STRING database

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Lars Juhl Jensen
Lars Juhl Jensen

Introduction to Bioinformatics, Heidelberg University, Heidelberg, Germany, November 29, 2006

Technologie
1 von 90
The STRING database Lars Juhl Jensen EMBL Heidelberg
data integration
Jensen et al., Drug Discovery Today: Targets, 2004
functional interactions
Bork et al., Current Opinion in Structural Biology, 2005
373 proteomes
Genome Reviews
RefSeq
Ensembl
model organism databases
genomic context methods
gene fusion
 
gene neighborhood
 
phylogenetic profiles
 
 
 
 
Cell Cellulosomes Cellulose
automation
scoring scheme
correct interactions
wrong associations
gene fusion
sequence similarity
 
gene neighborhood
sum of intergenic distances
 
phylogenetic profiles
SVD Singular Value Decomposition
Euclidian distance
 
raw quality scores
not comparable
sequence similarity
sum of intergenic distances
Euclidian distance
benchmarking
calibrate vs. gold standard
 
raw quality scores
probabilistic scores
curated knowledge
KEGG Kyoto Encyclopedia of Genes and Genomes
Reactome
MIPS Munich Information center for Protein Sequences
STKE Signal Transduction Knowledge Environment
primary experimental data
many sources
many parsers
physical protein interactions
BIND Biomolecular Interaction Network Database
GRID General Repository for Interaction Datasets
MINT Molecular Interactions Database
DIP Database of Interacting Proteins
HPRD Human Protein Reference Database
merge data by publication
topology-based scores
von Mering et al., Nucleic Acids Research, 2005
co-expression
GEO Gene Expression Omnibus
correlation coefficient
literature mining
different gene identifiers
synonyms lists
M EDLINE
SGD Saccharomyces Genome Database
The Interactive Fly
OMIM Online Mendelian Inheritance in Man
co-mentioning
NLP Natural Language Processing
[object Object],[object Object],[object Object],[object Object],[object Object]
calibrate vs. gold standard
 
combine all evidence
spread over many species
transfer by orthology
von Mering et al., Nucleic Acids Research, 2005
two modes
 
orthologous groups
von Mering et al., Nucleic Acids Research, 2005
fuzzy orthology
von Mering et al., Nucleic Acids Research, 2005
Bayesian scoring scheme
Bork et al., Current Opinion in Structural Biology, 2005
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]

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The STRING database