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.
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
