UCSC Genome Browser Sessions

Enhancer/Promoter regions were resized to 100/200 bp, respectively. Please refer to the 'FOCS predicted enhancer-promoter interactions' table below for the original sizes.


FOCS predicted enhancer-promoter interactions

Name (link) Species Description Type Size
FANTOM5 Enhancer-Promoter links with annotations Mouse (mm9) A tab-delimited text file. see README file for description in additional data below txt 8.4MB
FANTOM5 Enhancer-Promoter links with annotations Human (hg19) A tab-delimited text file. see README file for description in additional data below txt 6.5MB
GRO-seq Enhancer-Promoter links with annotations Human (hg19) A tab-delimited text file. see README file for description in additional data below txt 3.5MB
ENCODE Enhancer-Promoter links with annotations Human (hg19) A tab-delimited text file. see README file for description in additional data below txt 23MB
Roadmap Epigenomics Enhancer-Promoter links with annotations Human (hg19) A tab-delimited text file. see README file for description in additional data below txt 10MB

FANTOM5 data - Mouse (mm9)

Name (link) Description Type Size
Promoter-TSSs count profiles A matrix: rows are promoter-TSSs, columns are samples (Library id) RData 49MB
Promoter-TSSs normalized profiles A matrix: rows are promoter-TSSs, columns are samples (Library id) RData 69MB
Promoter genomic positions (genome build: mm9) A GRanges object: entries are promoter-TSSs, each entry contains chromosome, start and end positions, name, and more RData 2.8MB
Sample annotation A matrix: rows are samples, columns represent sample information (lib_id, cell_type, and lib_size) RData 14KB
Promoter-TSS's candidate enhancers in a fixed window A list: entries are Promoter-TSSs. Each entry contains the set of enhancer indices within a fixed window around the Promoter-TSS RData 945KB
Enhancer-TSSs count profiles A matrix: rows are enhancer-TSSs, columns are samples (Library id) RData 9.7MB
Enhancer-TSSs normalized profiles A matrix: rows are enhancer-TSSs, columns are samples (Library id) RData 12MB
Enhancer genomic positions (genome build: mm9) A GRanges list: entries are enhancer-TSSs, each entry contains chromosome, start and end positions, name, and score RData 1.1MB
Enhancer-Promoter links A list. Each entry of promoter-TSS is a vector of indexes in enhancer GRanges list RData 260KB

FANTOM5 data - Human (hg19)

Name (link) Description Type Size
Promoter-TSSs count profiles A matrix: rows are promoter-TSSs, columns are samples (Library id) RData 79MB
Promoter-TSSs normalized profiles A matrix: rows are promoter-TSSs, columns are samples (Library id) RData 110MB
Promoter genomic positions (genome build: hg19) A GRanges object: entries are promoter-TSSs, each entry contains chromosome, start and end positions, name, and more RData 2.9MB
Sample annotation A matrix: rows are samples, columns represent sample information (lib_id, cell_type, and lib_size) RData 30KB
Promoter-TSS's candidate enhancers in a fixed window A list: entries are Promoter-TSSs. Each entry contains the set of enhancer indices within a fixed window around the Promoter-TSS RData 772KB
Enhancer-TSSs count profiles A matrix: rows are enhancer-TSSs, columns are samples (Library id) RData 18MB
Enhancer-TSSs normalized profiles A matrix: rows are enhancer-TSSs, columns are samples (Library id) RData 23MB
Enhancer genomic positions (genome build: hg19) A GRanges list: entries are enhancer-TSSs, each entry contains chromosome, start and end positions, name, and score RData 1.6MB
Enhancer-Promoter links A list. Each entry of promoter-TSS is a vector of indexes in enhancer GRanges list RData 218KB

GRO-seq data - Human (hg19)

Name (link) Description Type Size
Gene count profiles A matrix: rows are genes, columns are GEO samples RData 2.9MB
Gene normalized profiles A matrix: rows are genes, columns are GEO samples RData 8.9MB
Gene genomic positions (genome build: hg19) A GRanges object: entries are genes, each entry contains chromosome, start and end positions, gene_id, and more RData 380KB
Sample annotation A matrix: rows are samples, columns represent sample information (srr_id, cell_type, lib_size, and GEO_id) RData 4KB
Gene's candidate enhancers in a fixed window A list: entries are genes. Each entry contains the set of enhancer indices within a fixed window around the gene's TSS RData 2.3KB
Enhancer count profiles A matrix: rows are enhancers, columns are GEO samples RData 38MB
Enhancer normalized profiles A matrix: rows are enhancers, columns are GEO samples RData 105MB
Enhancer genomic positions (genome build: hg19) A GRanges list: entries are enhancers, each entry contains chromosome, start and end positions, and more RData 1.6MB
Enhancer-Promoter links A list. Each entry of gene is a vector of indexes in enhancer GRanges list RData 88KB

ENCODE data - Human (hg19)

Name (link) Description Type Size
Promoter-DHSs count profiles A matrix: rows are promoter-DHSs, columns are GEO samples RData 23MB
Promoter-DHSs normalized profiles A matrix: rows are promoter-DHSs, columns are GEO samples RData 29MB
Promoter genomic positions (genome build: hg19) A GRanges object: entries are promoter-DHSs, each entry contains chromosome, start and end positions, name, and more RData 2.7MB
Sample annotation A matrix: rows are samples, columns represent sample information (GEO_id, cell_type, and lib_size) RData 3.3KB
Promoter-DHS's candidate enhancers in a fixed window A list: entries are Promoter-DHSs. Each entry contains the set of enhancer indices within a fixed window around the Promoter-DHS RData 10MB
Enhancer-DHSs count profiles A matrix: rows are enhancer-DHSs, columns are GEO samples RData 78MB
Enhancer-DHSs normalized profiles A matrix: rows are enhancer-DHSs, columns are GEO samples RData 99MB
Enhancer genomic positions (genome build: hg19) A GRanges list: entries are enhancer-DHSs, each entry contains chromosome, start and end positions, name, and score RData 4.2MB
Enhancer-Promoter links A list. Each entry of promoter-DHS is a vector of indexes in enhancer GRanges list RData 921KB

Roadmap data - Human (hg19)

Name (link) Description Type Size
Promoter-DHSs count profiles A matrix: rows are promoter-DHSs, columns are GEO samples RData 18MB
Promoter-DHSs normalized profiles A matrix: rows are promoter-DHSs, columns are GEO samples RData 66MB
Promoter genomic positions (genome build: hg19) A GRanges object: entries are promoter-DHSs, each entry contains chromosome, start and end positions, name, and more RData 1.7MB
Sample annotation A matrix: rows are samples, columns represent sample information (GEO_id, cell_type, and lib_size) RData 5KB
Promoter-DHS's candidate enhancers in a fixed window A list: entries are Promoter-DHSs. Each entry contains the set of enhancer indices within a fixed window around the Promoter-DHS RData 6.3MB
Enhancer-DHSs count profiles A matrix: rows are enhancer-DHSs, columns are GEO samples RData 155MB
Enhancer-DHSs normalized profiles A matrix: rows are enhancer-DHSs, columns are GEO samples RData 595MB
Enhancer genomic positions (genome build: hg19) A GRanges list: entries are enhancer-DHSs, each entry contains chromosome, start and end positions, name, and score RData 6.2MB
Enhancer-Promoter links A list. Each entry of promoter-DHS is a vector of indexes in enhancer GRanges list RData 385KB

Additional data: analysis and external databases

Name (link) Description Type Size
README Describes the fields within each interactions.txt file txt 1KB
Gencode V10 TSS genomic positions (1) A GRanges list: entries are genes' transcription start sites (TSSs), each entry contains chromosome, start and end positions, and annotations. ENCODE/Roadmap promoter-DHSs were annotated based on this source. Positions are in hg19 genome build. RData 3.6MB
ChIA-PET interactions - first anchor position (2) A GRanges list: entries are the first anchors of the ChIA-PET interactions. Positions are in hg19 genome build. RData 5MB
ChIA-PET interactions - second anchor position (2) A GRanges list: entries are the second anchors of the ChIA-PET interactions. Positions are in hg19 genome build. RData 5MB
GTEx eQTLs genomic positions (3) A GRanges list: entries are single nucleotide polymorphisms (SNPs) annotated with ensembl/entrez gene ids. GTEx V6 and V6p significant snp-gene associations were used. Positions are in hg19 genome build. RData 175MB
A GTEx map A table. Each row in the table maps between GTEx variant_id to rs_id (SNP build: dbSNP142; Genome build: GRCh37p13/hg19) RData 147MB
FANTOM5 map between promoter-TSSs to eQTLs A list: entries are promoter-TSSs. Each entry contains a vector associated SNPs indices in GTEx eQTLs genomic positions. This is being used in FANTOM5 external validation. RData 40MB
Gencode V10 map between TSSs to eQTLs A list: entries are Gencode-TSSs (Ensembl gene ids). Each entry contains a vector associated SNP indices in GTEx eQTLs genomic positions. This is being used in ENCODE/Roadmap external validation. RData 54MB
A gene ID map A list of two mapping tables. The first table is an ensembl-entrez map. The second table is an ensembl-symbol map. RData 808KB

(1) ftp://genome.crg.es/pub/Encode/data_analysis/TSS/Gencodev10_TSS_May2012.gff.gz
(2) Xie X, Ma W, Songyang Z, Luo Z, Huang J, Dai Z, et al. CCSI: a database providing chromatin--chromatin spatial interaction information. Database. Oxford University Press; 2016;2016:bav124
(3) Consortium Gte, others. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science (80-. ). 2015;348:648–60