Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci

Résumé fourni par la source

This data accompanies our publication in which we integrate a statistics of coronary artery disease (CAD) genetics from over one million individuals (10.1038/s41588-022-01233-6) with epigenetic data from 45 cell types to identify genes and transcription factors whose regulation is affected by variants. We apply two statistical approaches and identify 1,580 candidate disease genes, including 23.5% non-coding RNA genes. Here, we provide the SupplementaryData files, as well as additional resources. The code for the analyses is available on GitHub. SupplementaryData1-Enhancer_metadata.xlsx: Metadata for epigenome data for all 45 cell types SupplementaryData2-EnhancerInteractions_hg38.zip: Folder with REMs per cell type and their target genes. One bed-file per cell type with all candidate CREs and their comma-separated target genes in the 4th column. SupplementaryData3-GWAS_CAD_SNVs_hg38.xls: List of all CAD-SNVs (hg38) SupplementaryData4-SNEEPTable_hg38.xls: SNEEP result table, contains SNVs, TFs, CREs and genes (hg38) SupplementaryData5-CandidateCADGenes.xlsx: Gene table with all the integrated information and additional gene lists: known CAD GWAS genes, genes found via colocalization analysis, active genes, excluded genes SupplementaryData6-CandidateCADGenes_gProfiler.tsv.gz: Complete GO result table of the candidate CAD genes SupplementaryData7-TFTable_oddsRatios.xlsx: TF table with enrichment across cell types and input to Fig. 3A SupplementaryData8-STARNET_DifferentialExpression.csv.gz: CAD STARNET differential expression SupplementaryData9-TFSNV_eQTL_Overlap_Fig3D.txt: Overlap of TF-SNVs with eQTLs SupplementaryData10-CADTFs_TargetGenes_gProfiler.xlsx: Complete GO result table of CAD-TF target genes SupplementaryData11.1-columns_description.xlsx, SupplementaryData11.2-Coloc_GTEx_STARNET_PPH_statistics.csv.gz: Colocalization analysis results: posterior probabilities of colocalization (PPH0–PPH4) for tested gene–tissue–trait pairs and. 11.1 explains the columns, 11.2 has the data. SupplementaryData12.1-columns_description.xlsx, SupplementaryData12.2-GWAS_eQTL_Colocalization.csv.gz: Colocalization analysis results: SNV-level summary statistics. 12.1 explains the columns, 12.2 has the data. SupplementaryData13-GWAS_Phenotypes.xlsx: List of GWAS sources with CAD-relevant phenotypes SupplementaryData14-Primers.xlsx: List of primers for PCR and RT-qPCR SupplementaryData15_SNVs_IQCH_AS1_locus_coloc.xlsx: SNVs in the IQCH-AS1 locus shown in Fig. 4F SupplementaryData16-CDKN2B_AS1_CREs_hg38.xlsx: CREs and their target genes around CDKN2B-AS1, shown in Supplementary Fig. 3 SNPsnap_ld0.8_collection.tab.gz: contains all SNVs with LD >= 0.8 used to identify matching SNVs (default file from original SNPsnap implementation 10.1093/bioinformatics/btu655)

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