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Interaction Confidence Scoring Tool


   1. Input interaction network

Select a file containing your network
(one interaction per row; file size limit: 5 MB)
                 
Does your file contain a header row? (select for yes)
Text delimiter

Alternatively, paste interactions here
   2. Methods and parameters

2.1. Topology-based methods
 
CAPPIC
 
Assigns weights to edges according to graphical co-clustering of their incident nodes. Score range: [0, 1].
publications Kamburov et al., BMC Bioinformatics, 2012
 
Common neighbors
 
Assigns weights to edges according to the number of common network neighbors of their incident nodes. Score range: [0, 1].
publications Goldberg and Roth, PNAS, 2003
 
Geometric embedding
 
Embeds the network in a geometric space and weights edges according to the distance between their incident nodes in that space. Score range: [0, 1].
publications Kuchaiev et al., PLoS Comput. Biol., 2009
2.2. Annotation-based methods
 
Literature evidence
 
Number of publications reporting each interaction. ConsensusPathDB is used as the literature annotation basis. Score range: [0, ∞).
publications Kamburov et al., Nucleic Acids Res., 2011
 
GO semantic similarity
 
Semantic similarity of the Gene Ontology annotation of interacting genes. Score range: [0, 1].
publications Yu et al., Bioinformatics, 2010
 
Pathway co-occurrence
 
Indicates whether interaction participants are found together in manually annotated pathways. ConsensusPathDB is used as the pathway annotation basis. Score range: {0, 1} (discrete).
publications Kamburov et al., Nucleic Acids Res., 2011

   3. Integrate scores

 
Calculate aggregate scores
 
Integrates results from different scoring methods into an aggregate score through machine learning techniques. Score range: [0, 1].
publications Kamburov et al., Nucleic Acids Res., 2011

   4. Submit

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Contact: Dr. Atanas Kamburov, kamburov@molgen.mpg.de, +49 30 8413 1744.
Article: Kamburov, A., Stelzl, U., and Herwig, R. (2012) IntScore: a web tool for confidence scoring of biological interactions. Nucleic Acids Res. 40:W140-6.
Licensing: This website is free and open to all users and there is no login requirement. The Geometric embedding scoring method is restricted for academic use only.
Disclaimer: Neither the intScore developers nor the Max Planck Society are responsibile for the correctness or usefulness of the provided data.