EN-TEx portal

The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models
Ancillary files for the resource. Further details about each file is in the paper's STAR Methods. The files are organized here by section in the STAR Methods.


Personal Genome Construction


714K imprinted_genes_in_ENTEx_ASE.tsv All known imprinted genes for which allele-specific expression was detected, genome-wide, in the EN-TEx samples.
5.4K phased_block.tar.gz Parental origin of each phased block in the four individuals.

Functional Genomics Data Stack


5.2G fithic2_out.tar.gz Hi-C genomic data processed by Fit-Hi-C software.
148K TopDomTADcalls.tar.gz Topologically associating domains of the genome identified by TopDom software.
34M Supp_data_proteomics.xlsx Proteomics result summary including peptide annotation.

Comparison Between Personal and Reference Genomes


7.4K table.DE.genes.tsv Union of genes differentially expressed between reference and personal genomes across the four EN-TEx individuals.
3.9K table.DE.genes.techReps.liver.tsv Union of genes differentially expressed between reference and personal genomes across seven EN-TEx RNA-seq experiments with available replicates.
3.2K table.DE.genes.GM12878.tsv Genes differentially expressed between reference and personal genome in GM12878.
216K differentially_marked_H3K27ac_cCREs.txt Union of candidate cis-regulatory elements with differential H3K27ac signal between reference and personal genomes across the four EN-TEx individuals.

Variation Analysis of cCRE Activity


69K Similarity_of_functional_genomic_activities_of_cCREs.xlsx Similarities between all the available histone modifications.
301K normalized_proteomics_RNA-seq.dat Normalized proteomics and RNA-seq data of genes.

Calling AS Events


206M sample_signal_track.tar.gz Example output of haplotype-specific signal tracks.
39G AlleleSeq2_workflow_examples.tar.gz AlleleSeq2 workflow demonstrated using RNA-seq and H3K27ac ChIP-seq experiments from ENC-003 thyroid gland samples.
2.5G hetSNVs_default_AS.tsv Full list of accessible heterozygous SNV loci with haplotype-specific read counts.
1.9G hetSNVs_default_AS_DNase.tsv Full list of accessible heterozygous SNV loci with haplotype-specific read counts from the DNase-seq datasets.
3.8G ENTEx.TissueStacked.phased.final.txt Assessment of allelic imbalance in CpG methylation.
90G hic_files.tar.gz Allele-specific Hi-C interactions.

AS Functional Elements


94M genes_default_AS.tsv List of accessible genes with haplotype-specific read counts.
711M cCREs_default_AS.tsv List of accessible regulatory elements with haplotype-specific read counts.
11K Associated_AS_Disease_Genes.xlsx Allele-specific genes associated with diseases.

Aggregation of AS Events Across Tissues and Assays


8.6G hetSNVs_pooled_AS.tsv List of accessible hetSNVs with haplotype-specific read counts pooled across tissues.
1.9G hetSNVs_pooled_AS_DNase.tsv List of accessible hetSNVs with haplotype-specific read counts pooled across tissues from the DNase-seq datasets.
991M ENTEx.TissueAggregated.final.txt Assessment of allelic imbalance in CpG methylation with haplotype-specific methylated and unmethylated homozygous CpGs pooled across tissues.

AS Catalog


2.7G pgenome_NA12878.tar.gz Personal genome for NA12878.
1.9G pgenome_STL-002.tar.gz Personal genome for STL002.
1.9G pgenome_STL-003.tar.gz Personal genome for STL003.
178M hetSNVs_high-confidence_AS.tsv List of hetSNVs with high-confidence allelic imbalance calculations.
10G hetSNVs_high-power_AS.tsv List of hetSNVs with the high-power allelic imbalance calculations.

Structural Variants


692K Supp_Data_SVs_associated_with_eQTL.xlsx List of SV associated with allele-specific expressed genes and eQTLs.

Decoration of cCREs from ENCODE


2.1G cCRE_histoneSignals_qnorm.tar.gz Normalized signal matrix of histone modifications in cCREs.
1.3G cCRE_decoration.matrix Candidate cis-regulatory elements annotated by the EN-TEx resource.
17M active.combined_set.txt.zip Active candidate cis-regulatory elements of all the human tissues.
2.6M bivalent.combined_set.txt.zip Candidate cis-regulatory elements that have both active and repressive signals.
15M repressed.combined_set.txt.zip Repressed candidate cis-regulatory elements of all the human tissues.
51M Repressive_cCRE_DNAmethy_repressiveHM.zip Binary tables showing whether the repressive cCREs are supported by DNA methylation or repressive histone modifications (H3K27me3 and H3K9me3) in each tissue type.
2.6K Repressive_cCRE_DNAmethy_repressiveHM_summary.csv Summary of the binary tables showing the number and percentage of the repressive cCREs with specific patterns of repressive epigenomic modifications (DNA methylation, H3K27me3 and H3K9me3) in each tissue type.
1.4M cCRE_DNAme_subset.tsv.zip A set of repressed cCREs with DNA methylation signals.
358K stringent.regions.MF.hg38.bed Stringent regions with high Matched Filter scores.
2.9M ENTEx_fully_repressed_regions_independent_of_cCREs.bed Genomic regions not containing any active regulatory elements and marked only by repressive histone marks, not by active marks or transcriptional activity.

Tissue Specificity


226K Tissue_Specificity.zip The tissue specificity of gene expression and functional signals of cis-regulatory elements.

Relating Encyclopedia Decorations to QTLs and GWAS Loci


21M QTL_enrichment.zip The enrichment of QTL in cis-regulatory elements (cCREs).
5M GWAS_enrichment.zip GWAS enrichment of cis-regulatory elements (cCREs).

Compatibility Between Assays


251K Supp_Data_Compatibility.xlsx The compatibility of genes with ASE in each tissue and individual.
1.1M AS_ratios_and_eQTL_effect.tsv Compatibility between GTEx eQTLs and EN-TEx allele-specific expression and binding.

Extending eQTL Annotations to Hard-to-obtain Tissues


1.6-15G R6_RData.objects All transferQTL sub-models obtained using eQTLs from a given donor tissue.
1.1-11G R6_RData.4hm.objects All transferQTL sub-models obtained using chromatin features from only four histone marks (H3K36me3, H3K27ac, H3K4me1, H3K27me3), in addition to the non-chromatin features.
173M perTissue.likely.eQTLs.tsv Novel "likely" eQTLs in each target tissue predicted across all transferQTL submodels.
4.1G predictions.blood.eQTLs.tar.gz Predictions of transferQTL submodels using the blood eQTLs from Vosa et al., Nat Genet 2021.

Relation Between AS SNPs and TF Motifs


142K motif_ranking.tsv List of motifs with their odds ratio, p-values and rank in overall or in a specific assay.
35M SNPs_motif_cCRE.txt.gz Relationship among SNVs, motifs, and cis-regulatory elements.

Prediction of Promoter AS Activity With a Random Forest Model


133M ASB-predictions-on-GTEx-cohort.tsv.zip Results of allele-specific binding prediction model on GTEx.

Visualization of the EN-TEx Data


5G ENTEx.Explorer.cCRE.Combined.zip Candidate cis-regulatory elements used in EN-TEx.
21M ENTEx.Explorer.Expression.Combined.zip Expressed genes analyzed in EN-TEx.
1.6M ENTEx.Proteomics.cCRE.Combined.zip Results of mass spectrometry.