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Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes.


ABSTRACT:

Background

To understand the roles they play in complex diseases, genes need to be investigated in the networks they are involved in. Integration of gene expression and network data is a promising approach to prioritize disease-associated genes. Some methods have been developed in this field, but the problem is still far from being solved.

Results

In this paper, we developed a method, Networked Gene Prioritizer (NGP), to prioritize cancer-associated genes. Applications on several breast cancer and lung cancer datasets demonstrated that NGP performs better than the existing methods. It provides stable top ranking genes between independent datasets. The top-ranked genes by NGP are enriched in the cancer-associated pathways. The top-ranked genes by NGP-PLK1, MCM2, MCM3, MCM7, MCM10 and SKP2 might coordinate to promote cell cycle related processes in cancer but not normal cells.

Conclusions

In this paper, we have developed a method named NGP, to prioritize cancer-associated genes. Our results demonstrated that NGP performs better than the existing methods.

SUBMITTER: Wu C 

PROVIDER: S-EPMC3464615 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature

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Publications

Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes.

Wu Chao C   Zhu Jun J   Zhang Xuegong X  

BMC bioinformatics 20120728


<h4>Background</h4>To understand the roles they play in complex diseases, genes need to be investigated in the networks they are involved in. Integration of gene expression and network data is a promising approach to prioritize disease-associated genes. Some methods have been developed in this field, but the problem is still far from being solved.<h4>Results</h4>In this paper, we developed a method, Networked Gene Prioritizer (NGP), to prioritize cancer-associated genes. Applications on several  ...[more]

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