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Data integration and functional association networks

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Lars Juhl Jensen
Lars Juhl Jensen

Exploring Modular Protein Architecture, European Molecular Biology Laboratory, Heidelberg, Germany, December 3-5, 2008

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Lars Juhl Jensen Data integration and functional association networks
Lars Juhl Jensen Data integration and functional association networks
if this is your plan
 
 
STRING
Jensen, Kuhn et al., Nucleic Acids Research , 2009
data integration
functional associations
Frishman et al., Modern Genome Annotation , 2009
the basis
630 genomes
model organism databases
Ensembl
RefSeq
genomic context methods
gene fusion
Korbel et al., Nature Biotechnology , 2004
conserved neighborhood
Korbel et al., Nature Biotechnology , 2004
phylogenetic profiles
Korbel et al., Nature Biotechnology , 2004
primary experimental data
gene coexpression
 
GEO Gene Expression Omnibus
protein interactions
Jensen & Bork, Science , 2008
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
curated knowledge
complexes
MIPS Munich Information center for Protein Sequences
Gene Ontology
pathways
Letunic & Bork, Trends in Biochemical Sciences , 2008
KEGG Kyoto Encyclopedia of Genes and Genomes
MetaCyc
Reactome
PID NCI-Nature Pathway Interaction Database
literature mining
M EDLINE
SGD Saccharomyces Genome Database
The Interactive Fly
OMIM Online Mendelian Inheritance in Man
thesaurus
co-mentioning
 
NLP Natural Language Processing
[object Object],[object Object],[object Object],[object Object],[object Object]
too easy …
… to be true
many data types
not comparable
different error rates
many sources
different file formats
different gene identifiers
redundancy
spread over 630 genomes
raw quality scores
reproducibility
von Mering et al., Nucleic Acids Research , 2005
intergenic distances
Korbel et al., Nature Biotechnology , 2004
benchmarking
calibrate vs. gold standard
von Mering et al., Nucleic Acids Research , 2005
raw quality scores
probabilistic scores
transfer by orthology
von Mering et al., Nucleic Acids Research , 2005
two modes
COG mode
von Mering et al., Nucleic Acids Research , 2005
protein mode
von Mering et al., Nucleic Acids Research , 2005
combine all evidence
visualize
Frishman et al., Modern Genome Annotation , 2009
related resources
STITCH
 
protein–chemical network
 
Reflect
 
eggNOG
orthologous groups
 
NetworKIN
 
Linding, Jensen, Ostheimer et al., Cell , 2007
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],[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],[object Object],[object Object],[object Object],[object Object]

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Contenu connexe

Tendances

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Tendances (19)

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Systems biology - Understanding biology at the systems level
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En vedette

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En vedette (7)

A linear motif atlas for phosphorylation-dependent signaling
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Protein networks: A basis for large-scale data mining
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Disease Systems Biology
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