Prioritizing Chronic Obstructive Pulmonary Disease (COPD) Candidate Genes in COPD-related Networks

Overview

Journal Oncotarget

Specialty Oncology

Date 2017 Dec 22

PMID 29262568

Citations 3

Authors

Yihua Zhang

Wan Li

Yuyan Feng

Shanshan Guo

Xilei Zhao

Yahui Wang

Yuehan He

Weiming He

Lina Chen

Affiliations

Soon will be listed here.

Abstract

Chronic obstructive pulmonary disease (COPD) is a multi-factor disease, which could be caused by many factors, including disturbances of metabolism and protein-protein interactions (PPIs). In this paper, a weighted COPD-related metabolic network and a weighted COPD-related PPI network were constructed base on COPD disease genes and functional information. Candidate genes in these weighted COPD-related networks were prioritized by making use of a gene prioritization method, respectively. Literature review and functional enrichment analysis of the top 100 genes in these two networks suggested the correlation of COPD and these genes. The performance of our gene prioritization method was superior to that of ToppGene and ToppNet for genes from the COPD-related metabolic network or the COPD-related PPI network after assessing using leave-one-out cross-validation, literature validation and functional enrichment analysis. The top-ranked genes prioritized from COPD-related metabolic and PPI networks could promote the better understanding about the molecular mechanism of this disease from different perspectives. The top 100 genes in COPD-related metabolic network or COPD-related PPI network might be potential markers for the diagnosis and treatment of COPD.

Citing Articles

Candidate gene prioritization for chronic obstructive pulmonary disease using expression information in protein-protein interaction networks.

Li W, Zhang Y, Wang Y, Rong Z, Liu C, Miao H BMC Pulm Med. 2021; 21(1):280.

PMID: 34481483 PMC: 8418003. DOI: 10.1186/s12890-021-01646-9.

Identifying Protein-metabolite Networks Associated with COPD Phenotypes.

Mastej E, Gillenwater L, Zhuang Y, Pratte K, Bowler R, Kechris K Metabolites. 2020; 10(4).

PMID: 32218378 PMC: 7241079. DOI: 10.3390/metabo10040124.

A functional variant alters binding of activating protein 1 regulating expression of FGF7 gene associated with chronic obstructive pulmonary disease.

Zhang X, Guo Y, Yang J, Niu J, Du L, Li H BMC Med Genet. 2019; 20(1):33.

PMID: 30777021 PMC: 6380023. DOI: 10.1186/s12881-019-0761-7.

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