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