STRING database

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    STRING Database Known and Predicted Protein-Protein

    Interactions (PPIs)

    Mireia Calvo

    John Gonzlez

    Carles Navarro

    Bioinformatics, March 2014

    1

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    Index

    2

    STRING Database

    Database architecture

    Annotation Statistics

    Annotation format and example

    Curation

    Programmatic access

    Access condition

    Take fro mhttp://www.nature.com/

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    STRING Database

    3

    Search Tool for the Retrieval of Interacting

    Genes/Proteins (http://string-db.org/)

    2000

    Web-Server and

    Search Tool

    2009

    STRING 8

    URL-based programminginterface - API

    2011

    STRING 9.0 interactive network viewer

    3D structures

    third-party resources

    2013

    STRING v9.1

    automated mining

    Statistical enrichment

    2005

    + Data sources +scores

    Associations acrross

    organisms

    2003

    + Predictome and COG

    scoring scheme

    2007

    STRING 7

    AJAX-based web-navigation

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    Database architecture

    4

    PrimaryDatabases

    BIND, DIP, GRID,

    HPRD, IntAct andMINT

    Metadatabase

    PID

    PredictionDatabase

    STRING v9.1

    curated data from Biocarta, BioCyc,GO, KEGG, and Reactome

    STRING v9.1

    Items

    Proteins,species, COGs

    Network

    Nodes, edges,scores

    Evidence

    Datasets,abstracs,

    predictions

    Homology

    All-agains-allBLAST

    JSON (JavaScript Object Notation)

    *.tvs

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    Annotation Statistics

    5

    Latest version: 9.1 (2013)

    5,214,234 proteins

    1133 organisms

    >200 million interactions

    http://upload.wikimedia.org/wikipedia/commons/

    b/ba/Tree_of_Living_Organisms_2.png

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    Annotation format

    and example

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    Browser: name, identifier or aminoacid sequence of one or multiple proteins

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    Annotation format

    and example

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    Summary view: predicted associations, sorted by score

    o Input gene

    o Predicted Functional Partners

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    Annotation format

    and example

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    Selection of a gene: similar proteins

    Selection of a score bullet: breakdown of the individual prediction method

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    Annotation format

    and example

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    Combined association score

    Selected association: detailed evidence breakdown

    Selected protein: detailed information

    Network view

    o Red: fusion evidence

    o Green: neighborhood evidence

    o Blue: co-occurrence evidence

    o

    Purple: experimental evidenceo Yellow: textmining evidence

    o Light blue: database evidence

    o Black: coexpression evidence

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    Annotation format

    and example

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    Selected protein

    o Actionso Information

    o SMART domain

    o Protein structure

    o Identity

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    Annotation format

    and example

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    Neighborhood view

    Runs of genes occurring repeatedly in close

    neighbordhood in genomes

    Co-occurence view

    Linked proteins across species

    Fusion view

    Individual gene fusion events per species

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    Annotation format

    and example

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    Coexpression view

    Genes coexpressed in the same or in

    other species (transferred by homology)

    Experiments view

    Significant protein interaction datasets,

    gathered from other protein-protein

    interaction databases

    Databases view

    Significant protein interaction groups,gathered from curated databases

    Textmining view

    Significant protein interaction groups,

    extracted from the abstracts and scientific

    literature

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    Curation

    13

    Data source

    o Imported data (COG, Ensembled, Biocarta, KEGG, Swissprot)

    o Text mining

    o Predicted data

    Inside COG data base manually

    Outside COG data base automatically

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    Programmatic access

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    Web-browser API

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    Access condition

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    Four types of licence

    Commercial license

    Academic license

    Creative Commons Attribution 3.0 License

    Creative Commons Attribution-Noncommercial-Share Alike 3.0 License

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    References

    16

    [1] Franceschini A, Szklarczyk D, Frankild S, Kuhn M, Simonovic M, Roth A, Lin J, Minguez P, Bork P, von Mering C, Jensen LJ.,

    STRING v9.1: protein-protein interaction networks, with increased coverage and integration., Nucleic Acids Research, vol. 41, n

    Database issue, p. D808D815, 2013.

    [2] Szklarczyk D, Franceschini A, Kuhn M, Simonovic M, Roth A, Minguez P, Doerks T, Stark M, Muller J, Bork P, Jensen LJ, von Mering

    C., The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored., Nucleic Acids

    Reseach, vol. 39, n Database issue, pp. D561-8, 2011.

    [3] Jensen LJ, Kuhn M, Stark M, Chaffron S, Creevey C, Muller J, Doerks T, Julien P, Roth A, Simonovic M, Bork P, von Mering C.,

    STRING 8--a global view on proteins and their functional interactions in 630 organisms., Nucelic Acids Research, vol. 37, n

    Database issue, pp. D412-6, 2009.

    [4] von Mering C, Jensen LJ, Kuhn M, Chaffron S, Doerks T, Krger B, Snel B, Bork P., STRING 7--recent developments in the

    integration and prediction of protein interactions., Nucleic Acids Research, vol. 35, n Database issue, pp. D358-62, 2007.

    [5] von Mering C, Jensen LJ, Snel B, Hooper SD, Krupp M, Foglierini M, Jouffre N, Huynen MA, Bork P., STRING: known and

    predicted protein-protein associations, integrated and transferred across organisms., Nucleic Acids Research, vol. 33, n Database

    issue, pp. D433-7, 2005.

    [6] von Mering C, Huynen M, Jaeggi D, Schmidt S, Bork P, Snel B., STRING: a database of predicted functional associations between

    proteins, Nucleic Acids Research, vol. 31, n 1, pp. 258-61, 2003.

    [7] Snel B, Lehmann G, Bork P, Huynen MA., STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood

    of a gene., Nucleic Acids Research, vol. 28, n 18, pp. 3442-4, 200.

    [8] Javier De Las Rivas, Celia Fontanillo, ProteinProtein Interactions Essentials: Key Concepts to Building and Analyzing Interactome

    Networks, PLoS Computational Biology, vol. 6, no. 6, June 2010.

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    Thank you for your

    attention

    Questions?

    17