Difference between revisions of "Domain-based PPI network by Weighted Mutual Information (WMI)"

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Functional protein-protein interaction (PPI) networks elucidate molecular pathways underlying complex phenotypes, including those of human diseases. Extrapolation of domain-domain interac-tions (DDIs) from known PPIs is a major domain-based method for inferring functional PPI net-works. However, the protein domain is a functional unit of the protein. Therefore, we should be able to effectively infer functional interactions between proteins based on the co-occurrence of do-mains.
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Functional protein-protein interaction (PPI) networks elucidate molecular pathways underlying complex phenotypes, including those of human diseases.  
Here, we present a method for inferring accurate functional PPIs based on the similarity of domain composition between proteins by weighted mutual information that assigned different weights to the domains based on their genome-wide frequencies.  
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Protein domain is a functional unit of the protein. Therefore, we may effectively infer functional interactions between proteins based on the co-occurrence of domains.
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Here, we present a method for inferring accurate functional PPIs based on the similarity of domain composition between proteins by '''''weighted mutual information (WMI)''''' that assigned different weights to the domains based on their genome-wide frequencies.  
  
 
*[http://www.netbiolab.org/wiki/images/0/09/WMI_program.zip Source codes for WMI calculation]
 
*[http://www.netbiolab.org/wiki/images/0/09/WMI_program.zip Source codes for WMI calculation]
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*[http://www.netbiolab.org/wiki/images/4/44/HS_WMI_94K.txt Domain-based human PPI network by WMI]
 
*[http://www.netbiolab.org/wiki/images/4/44/HS_WMI_94K.txt Domain-based human PPI network by WMI]
  
''''Citation''''': Jung Eun Shim and Insuk Lee, Weighted mutual information analysis substantially improves domain-based functional network models '''''Under review'''''
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'''''Citation''''' : Jung Eun Shim and Insuk Lee, Weighted mutual information analysis substantially improves domain-based functional network models. Bioinformatics 2016 Sep 15;32(18):2824-30
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'''''Contact Information''''' : Insuk Lee (insuklee[at]yonsei[dot]ac[dot]kr)

Latest revision as of 16:29, 22 September 2017

Functional protein-protein interaction (PPI) networks elucidate molecular pathways underlying complex phenotypes, including those of human diseases. Protein domain is a functional unit of the protein. Therefore, we may effectively infer functional interactions between proteins based on the co-occurrence of domains. Here, we present a method for inferring accurate functional PPIs based on the similarity of domain composition between proteins by weighted mutual information (WMI) that assigned different weights to the domains based on their genome-wide frequencies.

Citation : Jung Eun Shim and Insuk Lee, Weighted mutual information analysis substantially improves domain-based functional network models. Bioinformatics 2016 Sep 15;32(18):2824-30

Contact Information : Insuk Lee (insuklee[at]yonsei[dot]ac[dot]kr)

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