Abstract
DNA methylation in gene or promoter or gene body could restrict/promote the gene transcription. Moreover, methylation in the gene regions along with CpG island regions could modulate the transcription to undetectable gene expression levels. Therefore, it is necessary to investigate the methylation levels within the gene, gene body, CpG island regions and their overlapped regions and then identify the gene-based differentially methylated regions (GeneDMRs). Here, R package GeneDMRs aims to facilitate computing gene based methylation rate using next generation sequencing (NGS)-based methylome data. The user-friendly R package GeneDMRs is presented to analyze the methylation levels in each gene/promoter/exon/intron/CpG island/CpG island shore or each overlapped region (e.g., gene-CpG island/promoter-CpG island/exon-CpG island/intron-CpG island/gene-CpG island shore/promoter-CpG island shore/exon-CpG island shore/intron-CpG island shore). Here, we used the public reduced representation bisulfite sequencing (RRBS) data of mouse (GSE62392) for evaluating software and found novel biologically significant results to supplement the previous research. The R package GeneDMRs can facilitate computing gene based methylation rate to interpret complex interplay between methylation levels and gene expression differences or similarities across physiological conditions or disease states.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
List of abbreviations
- Adora1
- Adenosine A1 receptor gene
- CMP
- Common myeloid progenitor
- CpG
- Cytosine and guanine dinucleotide
- DEG
- Differentially expressed gene
- DMC
- Differentially methylated cytosine
- DMCpGi
- Differentially methylated CpG island
- DME
- Differentially methylated exon
- DMG
- Differentially methylated gene
- DMI
- Differentially methylated intron
- DMP
- Differentially methylated promoter
- DMR
- Differentially methylated region
- DMShore
- Differentially methylated CpG island shore
- DMW
- Differentially methylated window
- GeneDMRs
- Gene-based differentially methylated regions
- GEO
- Gene Expression Omnibus
- GRN
- Gene regulatory network
- LogFC
- Log fold change
- NCBI
- National Center for Biotechnology Information
- NGS
- Next generation sequencing
- PCR
- Polymerase chain reaction
- QC
- Quality control
- RRBS
- Reduced representation bisulfite sequencing
- UCSC
- University of California Santa Cruz
- WGBS
- Whole genome bisulfite sequencing