DOI: 10.5281/zenodo.18175838
title: 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:



YAME

KYCG Bioconductor 


Downloads:



hg38

mm10


Funding: NIH/NIGMS 5R35GM146978