A novel DNA methylation assay, HELP-tagging, has been recently described to use massively parallel sequencing technology for genome-wide methylation profiling. Massively parallel sequencing-based assays such as this produce substantial amounts of data, which complicate analysis and necessitate the use of significant computational resources. To simplify the processing and analysis of HELP-tagging data, a bioinformatic analytical pipeline was developed. Quality checks are performed on the data at various stages, as they are processed by the pipeline to ensure the accuracy of the results. A quantitative methylation score is provided for each locus, along with a confidence score based on the amount of information available for determining the quantification. HELP-tagging analysis results are supplied in standard file formats (BED and WIG) that can be readily examined on the UCSC genome browser.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1007/978-1-61779-424-7_7 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Histone Modifications and DNA Methylation in Psoriasis: A Cellular Perspective.
Clin Rev Allergy Immunol
January 2025
Department of Dermatology and Venereology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
In recent years, epigenetic modifications have attracted significant attention due to their unique regulatory mechanisms and profound biological implications. Acting as a bridge between environmental stimuli and changes in gene activity, they reshape gene expression patterns, providing organisms with regulatory mechanisms to respond to environmental changes. A growing body of evidence indicates that epigenetic regulation plays a crucial role in the pathogenesis and progression of psoriasis.
View Article and Find Full Text PDFA pan-cancer analysis: predictive role of ZNF32 in cancer prognosis and immunotherapy response.
Discov Oncol
January 2025
Department of Otolaryngology-Head and Neck Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China.
The zinc finger protein 32 (ZNF32) has been associated with high expression in various cancers, underscoring its significant function in both cancer biology and immune response. To further elucidate the biological role of ZNF32 and identify potential immunotherapy targets in cancer, we conducted an in-depth analysis of ZNF32. We comprehensively investigated the expression of ZNF32 across tumors using diverse databases, including TCGA, CCLE, TIMER2.
View Article and Find Full Text PDFEpigenetic modulation of social cognition: exploring the impact of methylation in brain-derived neurotrophic factor and oxytocin receptor genes across sex.
Sci Rep
January 2025
Section of Self, Affect and Neuroscience, Institute of Behavioral Science in Medicine, Yonsei University College of Medicine, Seoul, Republic of Korea.
Social cognition, which ranges from recognizing social cues to intricate inferential reasoning, is influenced by environmental factors and epigenetic mechanisms. Notably, methylation variations in stress-related genes like brain-derived neurotrophic factor (BDNF) and the oxytocin receptor (OXTR) are linked to distinct social cognitive functions and exhibit sex-specific differences. This study investigates how these methylation differences affect social cognition across sexes, focusing on both perceptual and inferential cognitive levels.
View Article and Find Full Text PDFHypomethylation of the low-density lipoprotein receptor class A domain containing 4 gene in rheumatoid arthritis.
Clin Immunol
January 2025
Department of Rheumatology, Qilu Hospital of Shandong University(Qingdao), Qingdao, China. Electronic address:
Background: Rheumatoid arthritis (RA) is a chronic inflammatory disease linked to epigenetic changes, particularly DNA methylation. While LDLRAD4 has been implicated in RA through GWAS, its role in RA via methylation remains unclear.
Objectives: To investigate LDLRAD4 methylation patterns in RA and evaluate its potential as a diagnostic and inflammatory biomarker.
The association of physical function and physical performance with DNA methylation clocks in oldest-old living in Singapore - the SG90 cohort.
J Gerontol A Biol Sci Med Sci
January 2025
Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456, Singapore.
Deoxyribonucleic acid (DNA) methylation (DNAm) clocks estimate biological age according to DNA methylation. This study investigated the associations between measures of physical function and physical performance and ten DNAm clocks in the oldest-old in Singapore. The SG90 cohort included a subset of community-dwelling oldest-old from the Singapore Chinese Health Study (SCHS) and Singapore Longitudinal Ageing Study (SLAS).
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!