Dataset for "KnowYourCG: Facilitating base-level sparse methylome interpretation" --- EPIC

Knowledgebases for the MethylationEPIC Array (EPIC v1.0)

This repository hosts curated knowledgebases for the Infinium MethylationEPIC (v1.0) array. These datasets are formatted as RDS files specifically for use with the knowYourCG Bioconductor package. They provide the necessary biological and technical context to perform functional enrichment analysis on EPIC array data.

1. Technical Metadata & Quality Control

Datasets describing the physical properties of the EPIC array and recommended filtering parameters.

• ProbeType — Infinium Type I vs Type II probe design.

• InfiniumChemistry — Technical chemistry metadata for the EPIC platform.

• Mask — Probes flagged for potential technical artifacts, SNPs, or cross-reactivity.

• Blacklist — Genomic regions known to produce anomalous or unreliable signals.

2. Genomic Context & Sequence Features

Knowledgebases defining the DNA sequence characteristics and genomic landmarks of the EPIC probes.

• CGI — CpG Island (CGI) associations.

• nFlankCG — Nucleotide composition of sequences flanking the targeted CpGs.

• Tetranuc2 — Tetranucleotide frequency signatures.

• rmsk1 & rmsk2 — RepeatMasker repetitive elements (SINEs, LINEs, LTRs, etc.).

3. Epigenomic States & Regulatory Elements

Functional annotations relating methylation sites to chromatin accessibility and gene regulation.

• ChromHMM & REMCChromHMM — Multi-tissue chromatin state models and Roadmap Epigenomics data.

• HM — Histone modification peak overlaps (e.g., H3K4me3, H3K27ac).

• TFBSrm — Transcription Factor Binding Sites.

• CTCFbind — CTCF binding and genomic insulator sites.

• ABCompartment — Higher-order chromatin A/B compartments.

• PMD — Partially Methylated Domains.

4. Biological Signatures & Special Features

Knowledgebases focused on specific biological phenomena and gene-level summaries.

• ImprintingDMR — Differentially Methylated Regions associated with genomic imprinting.

• MetagenePC — Principal components summarizing gene-level methylation profiles.

External Resources

• Software: knowYourCG (Bioconductor)

• User Guide: knowYourCG Vignette

• Background Paper: Goldberg and Fu et al., Science Advances (2025)