Dataset for "KnowYourCG: Facilitating base-level sparse methylome interpretation" --- hg38

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.cm + .idx - TFBS collection 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 YAME KYCG Bioconductor hg38 (this page) mm10 Funding: NIH/NIGMS 5R35GM146978KYCG 知识库集（hg38） 概述 本仓库包含适配KnowYourCG（KYCG）框架的全套知识库集，旨在实现碱基分辨率水平的功能性DNA甲基化分析。上述数据库可支持快速富集检验与多样甲基化数据集的注释解读，涵盖低覆盖度测序数据（低通量、单细胞测序）、5-羟甲基化（5hmC）谱、空间甲基组以及基于芯片的表观基因组全关联分析数据集。 引用文献：Goldberg DC、Fu H、Atkins D、Moyer E、Lee CN、Deng Y、Zhou W.（2025）。KnowYourCG：助力碱基分辨率稀疏甲基组解读。《Science Advances》11(43)。DOI:10.1126/sciadv.adw3027 参考坐标 cpg_nocontig.cr hg38版本下所有CpG位点的完整参考坐标（排除重叠群），是富集检验与坐标映射的核心基准文件。 I. 序列特征 nFlankCG.20220321.cm —— 标准侧翼区域的CpG计数 nFlankCG50.20231025.cm —— 50bp侧翼区域内的CpG计数 nFlankCG100.20231025.cm —— 100bp侧翼区域内的CpG计数 Tetranuc2.20220321.cm —— CpG位点周边的四碱基序列上下文 CGI.20220904.cm —— CpG岛注释信息 rmsk1.20220307.cm + .idx —— 第一类重复序列注释（RepeatMasker注释结果） rmsk2.20220321.cm + .idx —— 第二类重复序列注释（RepeatMasker注释结果） II. 基因组特征 Chromosome.20221129.cm —— 基础染色体注释 ChromosomeXY.20230901.cm —— 性染色体特异性特征 Centromere.20221129.cm —— 着丝粒区域注释 Win100k.20220228.cm —— 100kb基因组窗口注释 ABCompartment.20220911.cm —— A/B区室注释（开放/闭合染色质） PMD.20220911.cm —— 部分甲基化结构域 CTCFbind.20220911.cm —— CTCF结合位点（染色质环锚点） ChromHMM.20220303.cm —— 标准ChromHMM状态注释 ChromHMMfullStack.20230515.cm —— 多细胞类型下的全维度ChromHMM状态注释 REMCChromHMM.20220911.cm —— Roadmap表观基因组计划ChromHMM状态注释 HM.20221013.cm + .idx —— 全套组蛋白修饰标记（包含H3K4me3、H3K27ac、H3K9me3、H3K27me3等） MetagenePC.20220911.cm + .idx —— 基因特征相关的位置信息（涵盖启动子、基因本体、3'非翻译区等） TFBS.20220921.cm + .idx —— 转录因子结合位点合集 TFBSrm.20221005.cm + .idx —— Roadmap表观基因组计划转录因子结合位点（涵盖约1188种转录因子） RoadMapPosGeneExpCpG.20220814.cm —— 与基因表达呈正相关的CpG位点 RoadMapNegGeneExpCpG.20220814.cm —— 与基因表达呈负相关的CpG位点 III. 性状关联特征 TiSigBLUEPRINT.20221209.cm + .idx —— 造血细胞类型特征谱（血液谱系） TiSigBrain.20221209.cm + .idx —— 脑细胞类型特征谱（神经元、胶质细胞） TiSigLoyfer.20221209.cm + .idx —— 广谱组织与细胞类型图谱 ImprintingDMR.20220818.cm —— 基因组印记差异甲基化区域 IntermediateMeth.20221121.cm —— 甲基化水平处于25%-75%区间的CpG位点 IntermediateMethS.20221121.cm —— 稳定的中间甲基化位点 XCILinkedWGBS.20221121.cm —— 与X染色体失活相关的CpG位点 XCILinkedWGBSSorted.20221121.cm —— 排序后的X染色体失活关联位点 IV. 技术关联特征 Blacklist.20220304.cm —— 用于过滤的问题基因组区域（高覆盖度伪影、重复序列区域） 资源 YAME KYCG Bioconductor hg38（本页面） mm10 资助信息：美国国立卫生研究院/国立普通医学科学研究所 5R35GM146978