KnowYourCG: Facilitating base-level sparse methylome interpretation
David C. Goldberg, Hongxiang Fu, Daniel Atkins, Ethan Moyer, Chin Nien Lee, Yanxiang Deng, Wanding Zhou
TL;DR
KnowYourCG is a new tool that helps scientists interpret DNA methylation data at the base level, uncovering biological and technical insights.
Contribution
KnowYourCG introduces a CpG-based framework for base-level methylome analysis, enabling insights into diverse biological and technical factors.
Findings
KYCG enables base-level screening of methylation data for biological and technical influences.
The tool effectively handles sparse methylation datasets like single-cell and low-pass methylomes.
Applications of KYCG reveal insights into cancer origins, cell differentiation, and technical artifacts.
Abstract
Decoding DNA methylomes for biological insights is critical in epigenetics research. We present KnowYourCG (KYCG), a data interpretation framework designed for functional DNA methylation analysis. Unlike existing tools that target genes or genomic intervals, KYCG features direct base-level screenings of diverse biological and technical influences, including sequence motifs, transcription factor binding, histone modifications, replication timing, cell-type–specific methylation, and trait associations. Through implementing efficient infrastructure that rapidly screens and investigates thousands of knowledgebases, KYCG addresses the challenges of data sparsity in various methylation datasets, including low-pass or single-cell DNA methylomes, 5-hydroxymethylation (5hmC) profiles, spatial DNA methylation maps, and array-based datasets for epigenome-wide association studies. Applying KYCG to…
Genes, proteins, chemicals, diseases, species, mutations and cell lines named across the full text — each resolved to its canonical identifier and authoritative record.
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Taxonomy
TopicsEpigenetics and DNA Methylation · RNA modifications and cancer · Genomics and Chromatin Dynamics