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Flongle data for KnowYourCG: Facilitating base-level sparse methylome interpretation

Fu, Hongxiang12; Goldberg, David12; Zhou, Wanding12

Research facility: Children's Hospital of Philadelphia
Published Sep 10, 2025 on Dryad. https://doi.org/10.5061/dryad.zgmsbccq9

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Abstract

ONT-based 5mC and 5hmC signals across four mouse tissues (lung, blood, uterus, and cortex) profiled with low-pass Flongle flowcells (~1M CpGs per sample). 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 knowledge bases, KYCG addresses the challenges of data sparsity in various methylation datasets, including low-pass or single-cell DNA methylomes, 5-hydroxymethylation profiles, spatial DNA methylation maps, and array-based datasets for epigenome-wide association studies. Applying KYCG to these datasets provides valuable insights into cell differentiation, cancer origins, epigenome-trait associations, and technical issues such as array artifacts, single-cell batch effects, and Nanopore 5hmC detection accuracy. Our tool simplifies large-scale methylation analysis and integrates seamlessly with standard assay technologies.