Dataset for "KnowYourCG: Facilitating base-level sparse methylome interpretation" --- HM450

Knowledgebases for the HumanMethylation450 Array (HM450)

This repository hosts curated knowledgebases for the Infinium HumanMethylation450 (HM450) array. These datasets are specifically formatted as RDS files for the knowYourCG Bioconductor package. They enable researchers to perform functional enrichment analysis on 450k data using updated genomic landmarks, chromatin states, and regulatory features.

1. Technical Metadata & Quality Control

Essential datasets for array-level metadata and data cleaning.

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

• InfiniumChemistry — Technical chemistry metadata for the 450k platform.

• Mask (2026 Update) — Latest probe masking for artifacts and SNPs.

• Mask (Legacy, BioC default) — Previous version of quality masks.

• Blacklist — Genomic regions prone to mapping interference.

2. Genomic Context & Sequence Features

Knowledgebases describing the physical and evolutionary landscape of the 450k probes.

• Chromosome — Updated chromosomal assignments.

• CGI — CpG Island (CGI) associations.

• nFlankCG — Nucleotide composition of sequences flanking the CpG.

• Tetranuc2 — Tetranucleotide frequency signatures.

• rmsk1 & rmsk2 — RepeatMasker repetitive elements.

3. Epigenomic States & Regulatory Elements

Annotations linking 450k sites to functional chromatin and protein binding data.

• ChromHMM & REMCChromHMM — Chromatin state models and Roadmap Epigenomics updates.

• HM — Histone modification peak overlaps.

• TFBSrm — Transcription Factor Binding Sites.

• CTCFbind — CTCF binding/insulator sites.

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

• PMD — Partially Methylated Domains.

4. Biological Signatures

Specialized datasets for tissue-specific and developmental biology.

• ImprintingDMR — Differentially Methylated Regions associated with imprinting.

• MetagenePC — Principal components of gene-level methylation.

References & Support

• DOI: 10.5281/zenodo.18344496

• Software: knowYourCG (Bioconductor)

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