Functional gene networks based on the gene neighborhood in metagenomes

Chan Yeong Kim, In suk Lee

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

The gene neighborhood in prokaryotic genomes has been effectively utilized in inferring co-functional networks in various organisms. Previously, such genomic context information has been sought among completely assembled prokaryotic genomes. Here, we present a method to infer functional gene networks according to the gene neighborhood in metagenome contigs, which are incompletely assembled genomic fragments. Given that the amount of metagenome sequence data has now surpassed that of completely assembled prokaryotic genomes in the public domain, we expect benefits of inferring networks by the metagenome-based gene neighborhood. We generated co-functional networks for diverse taxonomical species using metagenomics contigs derived from the human microbiome and the ocean microbiome. We found that the networks based on the metagenome gene neighborhood outperformed those based on 1748 completely assembled prokaryotic genomes. We also demonstrated that the metagenome-based gene neighborhood could predict genes related to virulence-associated phenotypes in a bacterial pathogen, indicating that metagenome-based functional links could be sufficiently predictive for some phenotypes of medical importance. Owing to the exponential growth of metagenome sequence data in public repositories, metagenome-based inference of co-functional networks will facilitate understanding of gene functions and pathways in diverse species.

Original languageEnglish
Pages (from-to)301-306
Number of pages6
JournalAnimal Cells and Systems
Volume21
Issue number5
DOIs
Publication statusPublished - 2017 Sep 3

Fingerprint

Metagenome
Gene Regulatory Networks
Genes
genes
Genome
Microbiota
genome
Phenotype
Metagenomics
genomics
gene regulatory networks
phenotype
Public Sector
Oceans and Seas
Virulence
Pathogens
virulence
oceans

All Science Journal Classification (ASJC) codes

  • Animal Science and Zoology
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

@article{471c02cf4f2a4f77865b012bc32ebd53,
title = "Functional gene networks based on the gene neighborhood in metagenomes",
abstract = "The gene neighborhood in prokaryotic genomes has been effectively utilized in inferring co-functional networks in various organisms. Previously, such genomic context information has been sought among completely assembled prokaryotic genomes. Here, we present a method to infer functional gene networks according to the gene neighborhood in metagenome contigs, which are incompletely assembled genomic fragments. Given that the amount of metagenome sequence data has now surpassed that of completely assembled prokaryotic genomes in the public domain, we expect benefits of inferring networks by the metagenome-based gene neighborhood. We generated co-functional networks for diverse taxonomical species using metagenomics contigs derived from the human microbiome and the ocean microbiome. We found that the networks based on the metagenome gene neighborhood outperformed those based on 1748 completely assembled prokaryotic genomes. We also demonstrated that the metagenome-based gene neighborhood could predict genes related to virulence-associated phenotypes in a bacterial pathogen, indicating that metagenome-based functional links could be sufficiently predictive for some phenotypes of medical importance. Owing to the exponential growth of metagenome sequence data in public repositories, metagenome-based inference of co-functional networks will facilitate understanding of gene functions and pathways in diverse species.",
author = "Kim, {Chan Yeong} and Lee, {In suk}",
year = "2017",
month = "9",
day = "3",
doi = "10.1080/19768354.2017.1382388",
language = "English",
volume = "21",
pages = "301--306",
journal = "Animal Cells and Systems",
issn = "1976-8354",
publisher = "Taylor and Francis Ltd.",
number = "5",

}

Functional gene networks based on the gene neighborhood in metagenomes. / Kim, Chan Yeong; Lee, In suk.

In: Animal Cells and Systems, Vol. 21, No. 5, 03.09.2017, p. 301-306.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Functional gene networks based on the gene neighborhood in metagenomes

AU - Kim, Chan Yeong

AU - Lee, In suk

PY - 2017/9/3

Y1 - 2017/9/3

N2 - The gene neighborhood in prokaryotic genomes has been effectively utilized in inferring co-functional networks in various organisms. Previously, such genomic context information has been sought among completely assembled prokaryotic genomes. Here, we present a method to infer functional gene networks according to the gene neighborhood in metagenome contigs, which are incompletely assembled genomic fragments. Given that the amount of metagenome sequence data has now surpassed that of completely assembled prokaryotic genomes in the public domain, we expect benefits of inferring networks by the metagenome-based gene neighborhood. We generated co-functional networks for diverse taxonomical species using metagenomics contigs derived from the human microbiome and the ocean microbiome. We found that the networks based on the metagenome gene neighborhood outperformed those based on 1748 completely assembled prokaryotic genomes. We also demonstrated that the metagenome-based gene neighborhood could predict genes related to virulence-associated phenotypes in a bacterial pathogen, indicating that metagenome-based functional links could be sufficiently predictive for some phenotypes of medical importance. Owing to the exponential growth of metagenome sequence data in public repositories, metagenome-based inference of co-functional networks will facilitate understanding of gene functions and pathways in diverse species.

AB - The gene neighborhood in prokaryotic genomes has been effectively utilized in inferring co-functional networks in various organisms. Previously, such genomic context information has been sought among completely assembled prokaryotic genomes. Here, we present a method to infer functional gene networks according to the gene neighborhood in metagenome contigs, which are incompletely assembled genomic fragments. Given that the amount of metagenome sequence data has now surpassed that of completely assembled prokaryotic genomes in the public domain, we expect benefits of inferring networks by the metagenome-based gene neighborhood. We generated co-functional networks for diverse taxonomical species using metagenomics contigs derived from the human microbiome and the ocean microbiome. We found that the networks based on the metagenome gene neighborhood outperformed those based on 1748 completely assembled prokaryotic genomes. We also demonstrated that the metagenome-based gene neighborhood could predict genes related to virulence-associated phenotypes in a bacterial pathogen, indicating that metagenome-based functional links could be sufficiently predictive for some phenotypes of medical importance. Owing to the exponential growth of metagenome sequence data in public repositories, metagenome-based inference of co-functional networks will facilitate understanding of gene functions and pathways in diverse species.

UR - http://www.scopus.com/inward/record.url?scp=85030330330&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85030330330&partnerID=8YFLogxK

U2 - 10.1080/19768354.2017.1382388

DO - 10.1080/19768354.2017.1382388

M3 - Article

VL - 21

SP - 301

EP - 306

JO - Animal Cells and Systems

JF - Animal Cells and Systems

SN - 1976-8354

IS - 5

ER -