Defiant

(DMRs: Easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus

David E. Condon, Phu V Tran, Yu Chin Lien, Jonathan Schug, Michael K Georgieff, Rebecca A. Simmons, Kyoung Jae Won

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Background: Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use extreme resources, and/or require library installation and input conversion. Results: We developed a new approach called Defiant to identify DMRs. Employing Weighted Welch Expansion (WWE), Defiant showed superior performance to other predictors in the series of benchmarking tests on artificial and real data. Defiant was subsequently used to investigate DNA methylation changes in iron-deficient rat hippocampus. Defiant identified DMRs close to genes associated with neuronal development and plasticity, which were not identified by its competitor. Importantly, Defiant runs between 5 to 479 times faster than currently available software packages. Also, Defiant accepts 10 different input formats widely used for DNA methylation data. Conclusions: Defiant effectively identifies DMRs for whole-genome bisulfite sequencing (WGBS), reduced-representation bisulfite sequencing (RRBS), Tet-assisted bisulfite sequencing (TAB-seq), and HpaII tiny fragment enrichment by ligation-mediated PCR-tag (HELP) assays.

Original languageEnglish (US)
Article number31
JournalBMC bioinformatics
Volume19
Issue number1
DOIs
StatePublished - Feb 5 2018

Fingerprint

Hippocampus
DNA Methylation
Iron
Annotation
Rats
Sequencing
Genes
Benchmarking
Neuronal Plasticity
Gene expression
Software packages
Libraries
Plasticity
Ligation
Assays
Software
Genome
Gene Regulation
Polymerase Chain Reaction
Software Package

Keywords

  • Bisulfite sequencing
  • DNA Methylation
  • Differentially Methylated regions (DMR)
  • Epigenetics
  • RRBS
  • WGBS

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural

Cite this

Defiant : (DMRs: Easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus. / Condon, David E.; Tran, Phu V; Lien, Yu Chin; Schug, Jonathan; Georgieff, Michael K; Simmons, Rebecca A.; Won, Kyoung Jae.

In: BMC bioinformatics, Vol. 19, No. 1, 31, 05.02.2018.

Research output: Contribution to journalArticle

@article{678cf0090a0c47649ea6cd8ea5e53901,
title = "Defiant: (DMRs: Easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus",
abstract = "Background: Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use extreme resources, and/or require library installation and input conversion. Results: We developed a new approach called Defiant to identify DMRs. Employing Weighted Welch Expansion (WWE), Defiant showed superior performance to other predictors in the series of benchmarking tests on artificial and real data. Defiant was subsequently used to investigate DNA methylation changes in iron-deficient rat hippocampus. Defiant identified DMRs close to genes associated with neuronal development and plasticity, which were not identified by its competitor. Importantly, Defiant runs between 5 to 479 times faster than currently available software packages. Also, Defiant accepts 10 different input formats widely used for DNA methylation data. Conclusions: Defiant effectively identifies DMRs for whole-genome bisulfite sequencing (WGBS), reduced-representation bisulfite sequencing (RRBS), Tet-assisted bisulfite sequencing (TAB-seq), and HpaII tiny fragment enrichment by ligation-mediated PCR-tag (HELP) assays.",
keywords = "Bisulfite sequencing, DNA Methylation, Differentially Methylated regions (DMR), Epigenetics, RRBS, WGBS",
author = "Condon, {David E.} and Tran, {Phu V} and Lien, {Yu Chin} and Jonathan Schug and Georgieff, {Michael K} and Simmons, {Rebecca A.} and Won, {Kyoung Jae}",
year = "2018",
month = "2",
day = "5",
doi = "10.1186/s12859-018-2037-1",
language = "English (US)",
volume = "19",
journal = "BMC Bioinformatics",
issn = "1471-2105",
publisher = "BioMed Central",
number = "1",

}

TY - JOUR

T1 - Defiant

T2 - (DMRs: Easy, fast, identification and ANnoTation) identifies differentially Methylated regions from iron-deficient rat hippocampus

AU - Condon, David E.

AU - Tran, Phu V

AU - Lien, Yu Chin

AU - Schug, Jonathan

AU - Georgieff, Michael K

AU - Simmons, Rebecca A.

AU - Won, Kyoung Jae

PY - 2018/2/5

Y1 - 2018/2/5

N2 - Background: Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use extreme resources, and/or require library installation and input conversion. Results: We developed a new approach called Defiant to identify DMRs. Employing Weighted Welch Expansion (WWE), Defiant showed superior performance to other predictors in the series of benchmarking tests on artificial and real data. Defiant was subsequently used to investigate DNA methylation changes in iron-deficient rat hippocampus. Defiant identified DMRs close to genes associated with neuronal development and plasticity, which were not identified by its competitor. Importantly, Defiant runs between 5 to 479 times faster than currently available software packages. Also, Defiant accepts 10 different input formats widely used for DNA methylation data. Conclusions: Defiant effectively identifies DMRs for whole-genome bisulfite sequencing (WGBS), reduced-representation bisulfite sequencing (RRBS), Tet-assisted bisulfite sequencing (TAB-seq), and HpaII tiny fragment enrichment by ligation-mediated PCR-tag (HELP) assays.

AB - Background: Identification of differentially methylated regions (DMRs) is the initial step towards the study of DNA methylation-mediated gene regulation. Previous approaches to call DMRs suffer from false prediction, use extreme resources, and/or require library installation and input conversion. Results: We developed a new approach called Defiant to identify DMRs. Employing Weighted Welch Expansion (WWE), Defiant showed superior performance to other predictors in the series of benchmarking tests on artificial and real data. Defiant was subsequently used to investigate DNA methylation changes in iron-deficient rat hippocampus. Defiant identified DMRs close to genes associated with neuronal development and plasticity, which were not identified by its competitor. Importantly, Defiant runs between 5 to 479 times faster than currently available software packages. Also, Defiant accepts 10 different input formats widely used for DNA methylation data. Conclusions: Defiant effectively identifies DMRs for whole-genome bisulfite sequencing (WGBS), reduced-representation bisulfite sequencing (RRBS), Tet-assisted bisulfite sequencing (TAB-seq), and HpaII tiny fragment enrichment by ligation-mediated PCR-tag (HELP) assays.

KW - Bisulfite sequencing

KW - DNA Methylation

KW - Differentially Methylated regions (DMR)

KW - Epigenetics

KW - RRBS

KW - WGBS

UR - http://www.scopus.com/inward/record.url?scp=85041394291&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85041394291&partnerID=8YFLogxK

U2 - 10.1186/s12859-018-2037-1

DO - 10.1186/s12859-018-2037-1

M3 - Article

VL - 19

JO - BMC Bioinformatics

JF - BMC Bioinformatics

SN - 1471-2105

IS - 1

M1 - 31

ER -