• Share
  • Email
  • Embed
  • Like
  • Save
  • Private Content
The STRING database
 

The STRING database

on

  • 677 views

14th International Conference on Intelligent Systems for Molecular Biology, Software demo, Fortaleza Conference Center, Fortaleza, Brazil, August 6-10, 2006

14th International Conference on Intelligent Systems for Molecular Biology, Software demo, Fortaleza Conference Center, Fortaleza, Brazil, August 6-10, 2006

Statistics

Views

Total Views
677
Views on SlideShare
677
Embed Views
0

Actions

Likes
0
Downloads
4
Comments
0

0 Embeds 0

No embeds

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

    The STRING database The STRING database Presentation Transcript

    • The STRING database Lars Juhl Jensen EMBL Heidelberg
    • data integration
    •  
    • functional interactions
    •  
    • 179 proteomes
    • Ensembl
    • SWISS-PROT
    • genomic context methods
    • phylogenetic profiles
    •  
    •  
    •  
    •  
    • Cell Cellulosomes Cellulose
    • gene fusion
    •  
    • gene neighborhood
    •  
    • questionable reliability
    • raw quality scores
    • gene neighborhood
    • sum of intergenic distances
    •  
    • many types of evidence
    • raw quality scores
    • not directly comparable
    • benchmarking
    • calibrate against KEGG
    •  
    • 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
    • parsers
    • co-expression
    • GEO Gene Expression Omnibus
    • SMD Stanford Microarray Database
    • 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
    • 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
      • Gene and protein names
      • Cue words for entity recognition
      • Verbs for relation extraction
      • [ nxgene The GAL4 gene ]
      • [ nxexpr T he expression of [ nxgene the cytochrome genes [ nxpg CYC1 and CYC7 ]]] is controlled by [ nxpg HAP1 ]
    •  
    • combine all evidence
    • spread over many species
    • transfer by orthology
    •  
    • orthologous groups
    •  
    • fuzzy orthology
    • ? Source species Target species
    • Bayesian scoring scheme
    •  
    • Acknowledgments
      • The STRING team (EMBL)
        • Christian von Mering
        • Berend Snel
        • Martijn Huynen
        • Sean Hooper
        • Samuel Chaffron
        • Julien Lagarde
        • Mathilde Foglierini
        • Peer Bork
      • Literature mining project (EML Research)
        • Jasmin Saric
        • Rossitza Ouzounova
        • Isabel Rojas