Published October 24, 2025
| Version v1
Dataset
Open
Dataset for "KnowYourCG: Facilitating base-level sparse methylome interpretation" --- hg38
Description
KYCG Knowledgebase Sets (hg38)
Overview
This repository contains comprehensive knowledgebase sets for the KnowYourCG (KYCG) framework, designed for functional DNA methylation analysis at base-level resolution. These databases enable rapid enrichment testing and interpretation of diverse methylation datasets, including sparse sequencing data (low-pass, single-cell), 5-hydroxymethylation (5hmC) profiles, spatial methylomes, and array-based EWAS datasets.
Citation: Goldberg DC, Fu H, Atkins D, Moyer E, Lee CN, Deng Y, Zhou W. (2025). KnowYourCG: Facilitating base-level sparse methylome interpretation. Science Advances 11(43). DOI: 10.1126/sciadv.adw3027
Reference Coordinates
cpg_nocontig.cr
- Complete reference coordinates for all CpG sites in hg38 (excluding contigs)
- Essential baseline for enrichment testing and coordinate mapping
I. Sequence Features
- nFlankCG.20220321.cm - CpG count in flanking regions (standard window)
- nFlankCG50.20231025.cm - CpG count within 50bp flanking regions
- nFlankCG100.20231025.cm - CpG count within 100bp flanking regions
- Tetranuc2.20220321.cm - Four-base sequence context surrounding CpG sites
- CGI.20220904.cm - CpG island annotations
- rmsk1.20220307.cm + .idx - RepeatMasker annotations (class 1)
- rmsk2.20220321.cm + .idx - RepeatMasker annotations (class 2)
II. Genomic Features
- Chromosome.20221129.cm - Basic chromosome annotations
- ChromosomeXY.20230901.cm - Sex chromosome-specific features
- Centromere.20221129.cm - Centromeric regions
- Win100k.20220228.cm - 100kb genomic window annotations
- ABCompartment.20220911.cm - A/B compartment annotations (open/closed chromatin)
- PMD.20220911.cm - Partially Methylated Domains
- CTCFbind.20220911.cm - CTCF binding sites (chromatin loop anchors)
- ChromHMM.20220303.cm - Standard ChromHMM state annotations
- ChromHMMfullStack.20230515.cm - Comprehensive ChromHMM states across multiple cell types
- REMCChromHMM.20220911.cm - Roadmap Epigenomics ChromHMM states
- HM.20221013.cm + .idx - Comprehensive histone modification marks (H3K4me3, H3K27ac, H3K9me3, H3K27me3, etc.)
- MetagenePC.20220911.cm + .idx - Positional information relative to gene features (promoters, gene bodies, 3'UTRs)
- TFBS.20220921.Part1.cm + .idx - TFBS collection Part 1
- TFBS.20220921.Part2.cm + .idx - TFBS collection Part 2
- TFBSrm.20221005.cm + .idx - Roadmap Epigenomics TFBS (~1,188 transcription factors)
- RoadMapPosGeneExpCpG.20220814.cm - CpGs positively correlated with gene expression
- RoadMapNegGeneExpCpG.20220814.cm - CpGs negatively correlated with gene expression
III. Trait Associates
- TiSigBLUEPRINT.20221209.cm + .idx - Hematopoietic cell type signatures (blood lineages)
- TiSigBrain.20221209.cm + .idx - Brain cell type signatures (neurons, glia)
- TiSigLoyfer.20221209.cm + .idx - Broad tissue and cell type atlas
- ImprintingDMR.20220818.cm - Genomically imprinted differentially methylated regions
- IntermediateMeth.20221121.cm - CpGs with intermediate methylation levels (25-75%)
- IntermediateMethS.20221121.cm - Stable intermediate methylation sites
- XCILinkedWGBS.20221121.cm - X-chromosome inactivation-associated CpGs
- XCILinkedWGBSSorted.20221121.cm - Sorted XCI-linked sites
IV. Technical Associates
- Blacklist.20220304.cm - Problematic genomic regions for filtering (high coverage artifacts, repeats)
Resources
Documentation:
Downloads:
Funding: NIH/NIGMS 5R35GM146978
Files
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Additional details
Related works
- Is supplement to
- Dataset: 10.1126/sciadv.adw3027 (DOI)