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

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<big>We present a method for inferring accurate functional PPIs based on the similarity of domain compositions between proteins by ''weighted mutual information'' that assigned different weights to domains based on their genome-wide frequencies.
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Functional protein-protein interaction (PPI) networks elucidate molecular pathways underlying complex phenotypes, including those of human diseases.
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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.
Catapult is a computer algorithm for associating new genes with traits, phenotypes, and diseases. Catapult leverages hundreds of thousands of known individual gene-phenotype associations from humans, mice, yeast, Arabidopsis, and C. elegans, and interprets them with the aid of a genome-scale functional network of human genes (HumanNet) in a graph-based formalism in order to rank new candidate genes
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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 calculating WMI]
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*[http://www.netbiolab.org/wiki/images/0/09/WMI_program.zip Source codes for WMI calculation]
*[http://www.netbiolab.org/wiki/images/1/1e/SC_WMI_12K.txt Yeast PPI network]
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*[http://www.netbiolab.org/wiki/images/1/1e/SC_WMI_12K.txt Domain-based yeast PPI network by WMI]
*[http://www.netbiolab.org/wiki/images/4/44/HS_WMI_94K.txt Human PPI network]
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*[http://www.netbiolab.org/wiki/images/4/44/HS_WMI_94K.txt Domain-based human PPI network by WMI]
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Citation: Jung Eun Shim and Insuk Lee, Weighted mutual information analysis sub-stantially 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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