Dataset for "KnowYourCG: Facilitating base-level sparse methylome interpretation" --- MM285

Knowledgebases for the Mouse Methylation BeadChip (MM285)

This repository hosts curated knowledgebases for the Mouse Methylation BeadChip (MM285). These datasets are specifically formatted as RDS files for the knowYourCG Bioconductor package to facilitate functional enrichment analysis in murine studies.

1. Technical Metadata & Quality Control

Datasets defining the physical architecture and data cleaning parameters specific to the mouse array.

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

• InfiniumChemistry — Technical chemistry metadata for the MM285 platform.

• ProbeCGnum — Number of CpGs queried by each probe.

• Mask — Probes flagged for potential technical artifacts or SNPs.

• Blacklist — Genomic regions known to produce poor quality or ambiguous data.

2. Genomic Context & Sequence Features

Mouse genomic landmarks and underlying DNA sequence characteristics.

• Chromosome — Murine chromosomal assignments.

• CGI — CpG Island (CGI) associations.

• nFlankCG — Flanking sequence composition.

• Tetranuc2 & Tetranuc4 — Tetranucleotide frequency signatures.

• rmsk1 & rmsk2 — RepeatMasker repetitive elements in the mouse genome.

3. Epigenomic States & Regulatory Elements

Functional annotations based on mouse-specific chromatin and transcription factor data.

• ChromHMM — Mouse-specific chromatin state models.

• EnsRegBuild — Ensembl Regulatory Build annotations.

• HM — Histone modification peaks for the mouse genome.

• TFBSrm — Transcription Factor Binding Sites.

• PMD — Partially Methylated Domains.

4. Biological Signatures

Knowledgebases summarizing gene-level and tissue-specific patterns.

• MetagenePC — Principal components of gene-level methylation profiles in mice.

References & Documentation

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

• Software: knowYourCG (Bioconductor)

• User Guide: Usage for Mouse Methylation Array